You need to use xdg-desktop-portals as well as gnomes backend for it so that metadata cleaner can access your files. This is a paper cut that shouldn't exist (xdg-desktop-portals should be installed alongside any distro that has flatpak, or made a dependency of flatpak when you are installing) but metadata cleaner does not need flatseal to work, and it was never intended to use filesystem=host in the first place.
You need to use xdg-desktop-portals as well as gnomes backend for it so that metadata cleaner can access your files. This is a paper cut that shouldn't exist (xdg-desktop-portals should be installed alongside any distro that has flatpak, or made a dependency of flatpak when you are installing) but metadata cleaner does not need flatseal to work, and it was never intended to use filesystem=host in the first place.