It appears Steam can't access all files

I was about to Add a Non-Steam App in my Library after finding out the location of the .desktop files and i can’t find ~/flatpak in sysroot when i access it in Steam, when in File Manager, it’s there. Is there a way to fix this?

I assume that you want to add games downloaded from the App Center to your Steam Library as Non-Steam games. This will not work, because Steam itself runs sandboxed (by Flatpak) and a sandboxed application can’t start another sandboxed one.

Technical Background for the interested ones

Flatpak relies on bwrap to set up the sandbox. On creation, bwrap is called with the appropriate parameters to set up a very nailed down environment with just the bare minimum required to run the application in question - normally this applications do not even have access to any regular user files (this is done through so called portals).

Now if a sandboxed application wants to run another sandboxed one, it would have to use bwrap to set up the environment for this application. But as it’s already sandboxed, it can’t do this as it has no permission to do so.