Ahh, that makes sense. So yeah, looks like the best option for now is as you stated, map the library to both the docker and native client (or keep separate libraries and sync them), but never have the docker active when using the native client.
Looks like managing remote instances is on the Calibre development roadmap, at least:
https://github.com/kovidgoyal/calibre/blob/master/src/calibre/srv/TODO.rst