flatpak: thanks to Make /sys hardening optional and allow access to /sys/fs to make polkit work by DanWin · Pull Request #204 · Kicksecure/security-misc · GitHub this is now fixed. Also discussed here: improve hide-hardware-info.service, make `/sys` hiding optional and enable by default · Issue #172 · Kicksecure/security-misc · GitHub
This is now in the testers repository.