In my case MODx is split frontend and backend, let me explain:
Frontend - The index.php pointing to a core on several web servers.
Backend - The actual CMS (IE the content of the manager folder) on a different server.
So to upgrade I need to do it piecemeal, which for me is painful.
I think u could just use the advanced installer out of the box, and just make it aware of your new core location?
RE the version number changing, possibly cache. Look in the DB table in modx_system_settings and see if it has updated.
If so, at least the DB schema has been updated.
Splitting things like that is an interesting idea.
When I tried updating with the advanced distro, the version number did not change in the DB. I wouldn't mind that except that it makes me wonder what else didn't get upgraded. Also, the next upgrade will be misinformed about the version it's upgrading from unless I change the setting, and then it may skip necessary steps.