As a matter of fact, I don't prefer Flatpak because I prefer the plain-looking but solid Synaptic. I have not fully tested the Gnome Software Centre on Zorin 17 and still have concerns. This means that it is acceptable that only Firefox is installed with Flatpak. However, if more and more software cannot be managed with apt in the future, my problems will deepen. 
I always install and uninstall from the command line (so I can see all the dependencies... especially when uninstalling... that's saved me many, many times when uninstalling something innocuous (such as a command-line calculator or a font) also wanted to uninstall large swaths of Zorin OS), but I use Synaptic to look at what's on the machine, what's needed and what's not needed, so I can whittle down the install size to the absolute minimum necessary to do what I need done.
I use:
sudo apt purge -s {package}
... first, look at what's going to get purged, and if anything essential (basically, if it says 'Zorin' in the package name, it's a pretty good bet it's essential) is going to get purged, I don't proceed.
I don't use Flatpak or Snap, I've got both of them uninstalled and purged (and all Snap mounts unmounted and deleted) and on hold... because all of the software I've tried via Flatpak didn't run right, and Snap slows down the boot because of having to do multiple mounts.
Mixing up APT and Flatpak installs just makes it more difficult to manage the ecosystem, if one has Flatpak uninstalled but not on hold. If they're going to do that, they should at least make it clearly obvious that they're doing it, and give a person the ability to back out before dumping Flatpak onto a system that doesn't want it.
Now I'm wondering what an install of this type will do with Flatpak purged and on hold... will the install fail? Will it go through but the software just won't run?
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Flatpak and Snap have certain Pros - this is undeniable.
Much of that relates to the developers, though. Not so much to the users. I also install primarily from terminal. But if I switch distros and install using pacman or yum, I do not feel any different than if I install using apt. Many users install packages using a package manager. So they do not really feel the effects of whether or not a package is "distro agnostic" or not.
The developers feel that. The users don't.
In order to make these packages distro agnostic, the solution is to containerize them and make them carry their own needed dependencies. Which is supposed to be a Pro. But it can just as easily be a Con including failures of the package since it cannot communicate with the very system it is installed on, isolated access, more user aggravation in trying to solve that isolation, and strangely, the creation of security holes in the process. You would think that something double sandboxed would ultimately be more secure.
https://www.opencve.io/cve/CVE-2017-9780
https://lwn.net/Articles/885530/
https://access.redhat.com/security/cve/cve-2023-28101
What we are finally left with is a strong developer push for these containerized apps because they are beneficial to developers to reduce their workload, but not necessarily helpful to the users. There are cases when a Flatpak or Snap can benefit a user; such as when they do need a higher package version than their distro supports. This is not often... And for most users, this looks like some drama taking place some distance away from them.
It leaves them confused: They have questions. Will this affect them? Should they trust or not trust these packaging formats? They try to ask questions and when they do, they find themselves caught in the fire of the passion both sides have for the topic.
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Maybe I am unnecessarily nervous because of my dissatisfaction with Zorin 16's Gnome Software Center and Mozilla. I understand that Zorin OS has few choices in browsers that can be pre-installed, and that is beyond the power of a distro. 
Which browser are you using, if I may ask. I've been looking for a replacement for forever, but haven't found one that fits the bill. And now with the new manifests coming up next year, it seems Firefox may be the only option in the midst of all the Chromium based ones.
I think that this is a very common problem.
We all seem to run into this wall where several different browsers offer some of or even most of what we want, but not all. Other browsers offer what the first doesn't, but doesn't offer what the first one does.
I use an ungoogled Chromium as a "Settling for what is closest."
I used to use Waterfox... Until it got sold to a target market advertiser.
You can find a great many suggestions on the forum; From Thorium to Epiphany to Brave. In the end, I personally think that it does not really matter... Just find one that fits as much as you can stand and remember that they all suck.
I think Brave is the closest to what I want, my only issue is the Chromium base and what's coming next year. So I might just stick with Firefox. 
You can also have multiple browsers installed and use them where they are better fit.
For the better part of this year I've used Firefox, Brave and Epiphany, and I use them for a dedicated purpose. Firefox is by far the one that I use the most, so I've setup multiple profiles with different plugins, settings and narrow down the activity further.
From time to time I also jump into Vivaldi, Ungoogled Chromium, etc., but haven't really felt the need to do so in quite a while, this particular setup works for me.
I removed Snap and Flatpak from Z16. I do not wish to use them on Z17.
If you have an older machine with minimal hardware capacity then use of Snap and Flatpak are not welcome.
This discussion is interesting and informative. I will be monitoring this subject as development of Z17 progresses to production versions as I happily use Firefox and Thunderbird as apt's on Z16.3 Core. If not available in Z17, I will be unhappy.
I tried looking it up and all I seemed able to find was just that they are moving the issue tracker to a different domain... is there something I'm missing?
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Note that Zorin will never take away the ability to install things with apt, that would go against their visions but also would not benefit them at all. Firefox has been installed as a Flatpak most likely because they didn't want the snap to be shipped with Zorin.
Even if Firefox is gone from Ubuntu's repositories one day, ZorinOS will not stop you from getting it directly from mozilla.
Yeah, I think I've never really made clear what I'm talking about.
This video summarizes quite well what I mean:
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And just today I decided to give a try to ungoogled chromium. It's a shame, it seems to open and perform way faster than firefox, but I'd prefer having a working ad blocker over speed, so back to firefox
If I'm being honest, I am not sure how something like this took so long to happen: most of google's income comes from ads and the android version of chrome never had support for ad blockers (not an android limitation, as other chromium-based android browsers like Microsoft Edge have support for ad blockers. Even some webview-based ones do aswell). It was just a matter of time until they decided to try to do something against ad blockers for desktop chrome
Something tells me that most browsers based on chromium will most likely try to find any workaround to be unaffected or just switch to a different base (based on firefox instead of chromium? Both are open source; original base?). But in the end, we can only wait and see what happens with the chromium ecosystem
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The developers will want what is good for them, not necessarily what is good for the user.
Then, they try to convince the users that they are offering "improvements" to get the users to think that they want it. As some users fall for this tactic, they then promote these ideas to other users, doing the work for the developers for free, while carrying the illusion of legitimacy since it is not coming from the biased developers but from other users who seem more trustworthy.
If developers are pushing for something and have a series of support from some of the users, but have a lot of resistence and pushback from the rest of the users - It is a sign that this is what is happening. SystemD, Snap, Flatpak, Libadwaita, all fall into this grouping.
They are first pushed heavily by the Developers with a vested personal interest in it.
But as Linus Torvalds points out: It is the End User that is the only one that matters.
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I have found a problem in the Flatpak version of Firefox where I cannot substitute fonts in the Font Manager. Perhaps font settings are not applied because Flatpak sandboxes the application. It is also troublesome to see strange directories when trying to download files.
Do You have the same Problem with the Firefox .deb Version?
I found workaround.
In Flatseal, Add xdg-config/fontconfig:ro to File system > Other section.
Enable File system > All user files.
I'm using SRWare Iron (it's essentially Chrome with the Google phone-home corporate spyware neutered), and uBlock Origin ad-blocker.
I'm assuming, given that they neuter all Google phone-home corporate spyware, that they'll also provide a way for ad-blockers to continue to work (ie: change the manifest) once Chromium caves and allows ad blockers to be blocked.
Meanwhile, my browser continues blocking ads, and even if I have to program my own solution, I'll not allow my machine to be overtaken with pop-ups, pop-unders, flashing banner ads and all the other detritus that often pollutes web pages. I haven't seen an ad (on my computer or my phone) in ages, and I intend to keep it that way.
If a web page wants to make money, offer something of benefit to your users. Ads only benefit you, the person making that web page.
[Moderator Note:
Political Rant Removed]
I'm thinking about setting up a Raspberry Pi running a command-line Linux variant with Bind Response Policy Zones.
Then it's a simple matter to just set all our computers / phones to use that as the DNS server when connected to our LAN (or set the DNS server setting in the router to use that Pi and leave all the computer / phone connections as they are now), and ads are blocked everywhere on the LAN.
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