I've heard Portainer is pretty nice for this.

Not really

Prceeds to troll

Grrr a bunch of people who make and maintain the free software I use won't officially support me doing whatever I want, what's wrong with them!!

I'm pretty sure you can remove flatpaks just as easily as AppImages + you have the option to delete user data specific to that app. Kinda sounds like you get all the problems OP describes without a clean way to manage it all.

Informative and informal. Love it!