Yes, you'd use rpm-ostree install on some downloaded RPM after adding the repo manually in /etc for updates later (they really make it painful because layering system packages should always be a last resort).

You're doing things correctly already. If everything is working fine with all the applications installed in a containerized way (distrobox, flatpak, etc.) no need to mess with rpm-ostree.

100% I was in the same boat as you with the yearly Ubuntu refreshes, and that got so old. Now if there's an update the breaks something I just rollback and pin the working version until there's an update that works or I have time to troubleshoot the issue.