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For immutable image type setups like SteamOS, it totally makes sense, but I'm loathe to have a bunch of different versions of libraries around because Flatpak A still depends on them and hasn't been updated yet - but I'm not the target audience if I'm actually reading the list of everything pacman (or apt, yum, etc.) wants to update and actively reviewing and deciding what I'm about to proceed with. (Looking at you, holding back Mesa for months because of that SteamVR regression.)
Containerisation is potentially nice, for sure, for all the same reasons Docker or Podman are. It's also potentially a pain in the butt for all the same reasons, if you have something that really needs a whole lot of permissions in the first place. 😅
I remember the days when Windows Vista(?)'s incessant UAC prompts just pushed people into turning it off entirely, and while my (mostly Steam Deck) experience with Flatpak has never been that bad, I've had to mess with Flatseal more than I want to, for things that 'just worked' on my desktop. I think giving emulators access to Bluetooth and USB gamepads was one of them - minor stuff, but the kind of stuff you'd expect an emulator to have the appropriate permissions for out of the box.
tl;dr, Flatpak is a great option, but I'm not moving from distro-native package management any time soon, and that's okay, because it doesn't have to be an either-or, and that's why Linux (and BSD, etc.) are awesome. 🩷