Agreed - I’m much happier with my /files directory. Not to mention I have no interest in organizing my files by type (photos, documents, music). Instead I have directories like house, finances, podcasts, etc.
I just wish programs wouldn’t take the XDG directories so seriously and default to those locations. I’d rather they always default to last saved directory.
Have you tried rpm-ostree apply-live? https://coreos.github.io/rpm-ostree/apply-live/