Yes, the split is needed at least for some of the dirs. For example, two instances of Mopidy-Spotify/pyspotify/libspotify cannot share the same libspotify cache, which is located in the core/cache_dir.
None at all. The local/media_dir is just read from.
I don’t know, but I would guess so.
No, I think this should work.
One tip to minimize the duplicated configuration is to in the init script set:
CONFIG_FILES="/usr/share/mopidy/conf.d:/etc/mopidy/mopidy.conf:/etc/mopidy/mopidy1al.conf"
That way, you can keep any common configuration in /etc/mopidy/mopidy.conf and only override the configs that varies from server to server in /etc/mopidy/mopidy1al.conf.