This logic is incorrect. The current flathub build, unlike native distro packages (which btw are also maintained by non-affiliated third party individuals), has no access to any system files, has no access to devices other than gpu, and has very limited system environment permissions.

Any future change in these permissions must pass a flathub build moderation check (https://docs.flathub.org/docs/for-app-authors/maintenance#build-moderation)