Do you know about Flatseal? It's an application that lets you manage flatpak permissions. Until the portals system is fully working, weakening the sandboxing using Flatseal is what a lot of people do to make the apps work correctly.
Also, if you use KDE, the settings app has flatseal-like functionality built in.
Fedora has a pretty good amount of software in the repositories, so a lot of the time that's enough. When it's not, flatpak with flathub have most gui software covered, and outside of that, if we're talking about terminal or command line stuff, most of those have their own custom way to install them, or they just have self contained binaries that you can put in ~/.local/bin/.
I haven't run into many issues with flatpak like it sounds like you have, so that really covers a lot of it for me honestly.
For anyone who's interested in an alternative, check out https://codidact.com . It's much smaller right now, but it's open-source and the community is nice.
Honestly, owning up to it being a selfish decision deserves some respect. I'm a big proponent of free expression and avoiding censorship, but I took a gander at the kinda stuff they got over there and...
It's not even the views they hold that's my main problem. It's really that they're just so needlessly rude and aggressive, and as you pointed out, they seem to be a lot more censorship happy than here anyway. I would be more sympathetic to them if they were less censorship happy themselves, and if they were less mean.
I do want to stress that I hope you keep the number of blocked instances to a minimum, since I feel that it would be better if the Lemmy software had better tools for users to control what they block for themselves better, and also maybe just having "default" blocklists that users can disable, to keep the new-user experience nice, but yeah for that particular instance, I can't be too mad about it.