To ensure games run well on Linux either via Native Linux builds or Windows games with Proton, part of the magic is in the Steam Linux Runtime. A new version of it, the Steam Linux Runtime 4.0 was recently put up with some pretty big changes.
What’s the point of it? It ensures Steam and games run through Steam on Linux work properly across all the many different Linux distributions. Another secret Valve sauce for Linux. Well, not secret at all but you get my meaning I’m sure.
Flatpacks have permission issues due to the way they are structurally designed. Applications like Flatseal and Bottles allow you to remove those limitations, but it’s a lot easier to just install the client outside of Flatpack.
I’ve only had to use Flatseal a couple times to fix wonky permissions for Flatpaks, and I’m not even sure what Bottles has to do with them since Wine has nothing to do with Flatpak to the best of my knowledge