@oops4041555 You can have global permission overwrites in Flatseal and you need to export /var/lib/flatpak/exports/bin/ for system and ~/.local/share/flatpak/exports/bin for user.
@choehau_ara Most people that are trying to do so fall into the trap of wanting to redo everything (the toolkit, apps...), even if most people seem to only really have problems with the shell.