True Ubuntu and debian is standard and to this day many external Devs just provide .deb files or now even snaps XD

So layering, as far as I understood:

1. your OS on your PC, every package traced through OSTree as with using Git
2. an ostree remote, which is not directly a repository but the exact OS they build.
3. Your PC compares the packages with the packages there and downloads the diffs.
4. Your PC then builds another image, being exactly the one on their servers

If you install/layer additional RPMs, after 3. you have an additional step, where rpm-ostree also uses traditional Fedora repos and downloads regular RPMs to your system. You can use any regular Repos, even COPR but you need to add the .repo files manually to /etc/yum.repos.d/. RPMFusion has a fancy way where you layer a package and that handles the updating of the repo files to your current version, really nice.

So this package is installed along, and as its done through rpm-ostree its very well traced. It will do changes but an rpm-ostree uninstall PACKAGE will completely remove it again. If you are not entirely sure rpm-ostree reset will completely reset your system to be a mirror of the ostree remote.

If you have a background service, you could reset the system every month or so. Not necessary but this would make extra sure your system directories are not weirdly modified. You would do this through

rpm-ostree reset --install PACKAGE1 --install PACKAGE2

Or maybe that doesnt work, not sure, and you need

rpm-ostree reset && rpm-ostree install PACKAGE1 PACKAGE2

Here you can also remove added packages like Kwrite or firefox + firefox-langpacks