Granted, most of the apps I used were snap based, but some of them were flatpack.
Most of them were single-use “use this tool with flatpack” tools via github, so I really can’t remember what those were when they just didn’t work.
The ones I looked into why it didn’t work were always some filesystem permission stuff. Configurable? Sure. Not something you should be needing to do on first launch if you want to just use the tool? Absolutely
The biggest issue I remember I had was with Vorta, a GUI for borg. Which also just had massive filesystem issues (plus some settings saving issues, which I assume also is a FS issue). Having problems reading your filesystem is quite a problem when you want to use a tool that, well, needs to read your filesystem.
I’m honestly not really interested in stacking a pile of tools up that just didn’t work for me.
If you like flatpack, go ahead. More power to the people who do.
It’s just not a tool that I had any luck with. And I don’t really see a point in trying again for the forseeable future