If you're limited on space, Flatpak (and Snap and AppImage) are not the way to go, as their entire reason for existing is to pre-bundle dependencies for the software so that they run on as many linux systems as possible - but this bundling results in eating a lot of your storage. It's not even possible to tell beforehand a lot of the time, as the sizes shown in gnome Software and KDE's equivalent are just for that app itself, not the supporting runtimes and other bits that will also be downloaded if you don't already have them from other Flatpaks you installed previously.
In gnome Software, a lot of apps will have a little drop-down menu near the install button where you can pick which packaging format to use. Here's an example from my Fedora system:
The gnome devs are famously anti-user and so not only do they prioritise anything and everything over native packages, they don't actually expose the setting to change it in the GUI.
You can, however, tell it to prioritise native packages via terminal commands if you want. I wrote about it in another thread here:
You can then look at backing up the config directories of your installed Flatpaks and try to replace as many as possible with native packages.
Also, try running flatpak remove --unused every now and then to clear out anything that gets left behind between updates and manually uninstalling software. Until recently, there was a bug (that the devs tried very hard to not admit to) where old nvidia runtimes would not be uninstalled automatically and would just accumulate on your computer, and even after running flatpak remove --unused only the 64bit versions would be removed; you had to manually uninstall all their 32bit counterparts. This is now, thankfully, fixed, but I can't remember which version of Flatpak fixed this.