Yeah, I only use flatpak for GUI apps that don't need any special handling. To be fair, that's a decent number of the things I use most often: Firefox, Thunderbird, Signal, Kodi, Discord, Gimp, VLC. I think it's also how I installed some themes for KDE / Plasma.

Console stuff I've either done in a distrobox using the conventions of that OS (apt for the Ubuntu one, DNF for the Fedora one), or I've used homebrew. But, I haven't used too much homebrew because I want my "normal" console to be as unchanged as possible.

There are a few things I've used distrobox-export to make available outside the distrobox.

It took me a little while to understand how you're supposed to think about the system, but now that I think I get it, I really like it. My one frustration is that there's an nVidia driver bug that's affecting me, and nVidia has been unable to fix it for a few months. I think I'd be in exactly the same situation with a traditional distro. The difference is that if they ever fix it, I'll have to wait a couple of weeks until the fix makes it to the Bazzite stable build. I suppose I could switch to Bazzite testing and get it within days of it being fixed instead of weeks. Apparently just use a "rebase" command and reboot. But, I'm hesitant to do that because other than the nVidia driver, everything's so stable.