I used to have issues with like rpmfusion repos and the like, worst case you may need to now the packages you have layered, do an rpm-ostree reset, upgrade, then layer the packages again. There's a way to install the rpmfusion repos that didn't break updates, I forget if they've updated the docs on the site to use it, I stopped layering almost everything in favor of flatpak or toolbx.

It will if the repos are specific to a fedora release version. That's been a thing with rpmfusion in the past, not sure it still is.