Even though the 'systemd' USE flag for flatpak is disabled, flatpak install following systemd-related files: $ equery files flatpak | rg systemd /usr/lib/systemd /usr/lib/systemd/system /usr/lib/systemd/user /usr/lib/systemd/user-environment-generators /usr/lib/systemd/user-environment-generators/60-flatpak /usr/lib/systemd/user/flatpak-oci-authenticator.service /usr/lib/systemd/user/flatpak-portal.service /usr/lib/systemd/user/flatpak-session-helper.service Reproducible: Always
Gentoo policy is to include those files regardless of the systemd USE flag. You can use INSTALL_MASK to exclude those files, as described here: https://wiki.gentoo.org/wiki/Gentoo_Without_systemd#systemd_unit_files
Ok, thanks, I did not know that. Closing this bug.