When setting up a local mirror of the rhel-9-for-x86_64-appstream-rpms repo, I use "dnf reposync --download-metadata --newest-only". Then to clear out the old versions of packages, I followed https://access.redhat.com/solutions/4011571 (but made it "dnf repomanage"). That consistently downloads and deletes some module-related packages, such as php-common-8.1.8-1.module+el9.1.0+15877+c3862210.x86_64.rpm.

It seems that reposync's logic for --newest-only must not quite match repomanage's logic for --new.