You're not imagining it.
Vehicles where there is a separate chassis with its own identifier on it, you go to VTNZ / VINZ etc (compliance place) with the vehicle, and proof that you own both identities. They then link your body / chassis mismatch together. They select one identity (I don't know if they use body or chassis identity) which becomes The Vehicle. They then make behind the scenes computer notes, to ensure that the same vehicle doesn't get registered twice (so if you're using the body, they then ensure that the chassis identity isn't re-registered by somebody else using that same chassis/vin number.
I don't know how every scenario works, as I don't know everything about it.
For the Escort question which sparked the discussion: no, you can't legally pull the identifiers off another shell. Identifiers, plates, and chunk of metal with wheels all need to be from the same vehicle. Otherwise stolen and re-identified cars would be even more common than they currently are.