When php <some-maintenance-script> --wiki=<some-db> is used on MW-Vagrant, the DB parameter is silently ignored. This is not obvious, and it's hard to figure out what's happening and how it can be avoided.
The relevant change is 27253a2; the version before that was not user-friendly, but that can be fixed. (E.g. choose the main wiki if there are no others, show an error message with the correct usage otherwise. That's also a good place to educate users about foreachwiki.)