Hello Ladies and Gentlemen!
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and numerious other Situations where Flataks (and Snap's) were a Problem because of it's Format and limited Permissions, I would suggest to change the default Package Format in Gnome Software to the .deb/APT Package. That can avoid Permissions-related Issues. Especially for new Users who might not know about that.
To be clear: I don't want suggest to ban Flatpaks. I only want suggest to don't set them as default Package Format.
New users (like me) have to Google the differences:
Synaptic (GUI) and APT (CLI) are traditional, distribution-specific package managers for DEB files, offering tight system integration and small file sizes. Flatpak and Snap are universal, sandboxed, containerized formats (Flatpak faster/safer, Snap better for CLI/servers) designed to work across all distributions, often requiring more disk space.
Key Comparisons:
or if you don't want to read:
But not everyone does that and simply installs what is presented and doesn't even pay Attention about the Package Format. Or ignore it for the Time.
...so we then have to ask them how they installed the app when they report issues here. Sometimes having them list their Flatpak's and Snap's to find out. There must be a better way.
I think AppPackage
AppImage seems to be the best method of installing apps. The problem is that quite a few don't get integrated into the OS with icons in the Zorin search and in the dash. But that could be overcome by integrating something like GearLever in the OS.
Other than that I think *.deb is what I've had the best experience with.
Speaking as a "newbie" here. 
.deb or Zorin native apt, are more compact than Flatpak and Snap when you have limited drive space.
Now we have to ask them how the app is actually installed, not how they think they chose to install it. As some .debs are vectored to Snap or Flatpak versions. This is horrible. Makes Windows look saintly (well maybe not that good).
Did you mean App Image? If not I think you mean APT. Aptitude is anothet option to use via Terminal.
In respect of Flatpak, this is where Q4OS shines. It has a Software Installer shortcut in its Welcome screen and Flatpak is an option to install, not a default presence.
Personally OS's that include Synaptic Package Manager, and not a post install necessity are better. Devuan, MX-Linux, PCLOS, PCLOS Debian.
Yes, I meant AppImage, sorry about that.
Just as you did with the dashes to make a strikethrough, replace the four dash marks with the tilde mark, instead and that will give the strikethrough.
I can only agree. This is something that has now made me consider perhaps not staying on Zorin.
An example is using and updating VS Code that I need for work, which can be done excellently using the debian packages from Microsoft.
The process is VS Code alerts me that there's an update, I visit the download page, then click the downloaded debian package on my drive and it opens in "Software". From there I can install.
But once I've installed, the view in "Software" changes from showing install and what I would expect to be "open" or "unistall" to instead inexplicably offer "install", but from flatpack, even though I just installed the latest version using a debian package. This is very weird.
Flatpack is not a very good option in my experience. With flatpak it's difficult to get and follow update alerts within the software. And it hard to share clipboard content with other apps.
So the fact the Zorin has flatpack as the primary way of offering software, means that I have to work against the OS and manually search for debian packages and download them, instead of using the nice and conventient "Software" app. It's unfortunate that you can't get debian packages through "Software".
Being able to download and then update software easy is an important feature for me. Most apps one uses update all the time and it's nice if you can take care of that with a few clicks. Instead having to go the extra mile.
The Gnome-software does not manage .deb files downloaded from other sources. This means that while you can install and uninstall them using Gnome-software, they will not appear in the list of installed apps.
Gnome-software offers a wide variety of .deb packages. The vast majority of Zorin apt packages (with a few exceptions) are genuine .deb files.
If you don't like flatpaks or snaps you can remove those plugins from the gnome-software so that gnome-software only shows Zorin apt packages.
Well, You can get it through there but You have to switch the Package Format manually on an Entry. The Problem with that: When there isn't an APT Entry, You only see the Flatpak Option and then You have to search until You find a Program with an APT Option for download.
I don't have something against Flatpaks. I use them, too. It is nice to have for me. And the Updates over Gnome Software running fine for me so far, too. But using this as default isn't the right Thing I would think.