You can override permissions (there is even a GUI called Flatseal for that). You are also not able to do any of that with distro package managers like apt or dnf. Ultimately you need to trust either.
What I mean is that permissions and accesses concern the operating system, not the software packaging. I don't understand why flatpack needs to deal with those, providing a false (and pernicious) aura of protection. I already run third-party software inside containers or virtual machines. No need for a GUI nor a flatpack-only solution like flatseal. It just looks pointless.
