What I did to get rid of my mess, was to containerize service after service using podman. I mount all volumes in a unified location and define all containers as quadlets (systemd services). My backup therefore consists of the base directory where all my container volumes live in subdirectories and the directory with the systemd units for the quadlets.

That way I was able to slowly unify my setup without risking to break all at once. Plus, I can easily replicate it on any server that has podman.