I can only speak of experience with N.S.W RTA here but I'd guess other states regognition of ID numbers would be the same.
In N.S.W the RTA only regognises the subframe number as the Vehicle Identification Number or VIN to be short.They don't consider the body number on the ID plate as the VIN number.
That said,
There would be a lot of FB's getting around with replacement EK subframes that are now considered by the RTA to be an EK Holden just because they now have an EK subframe, although the car still is ( to the owner) an FB and still has FB body tags and still looks like an FB, the RTA now says its an EK Holden

.
Vice-versa with EK's getting around with FB subframes being classed by the RTA as now being an FB.
I think Reddo's ute was an example.
It was an EK but had an FB subframe so according to the RTA it was an FB ( or vice-versa ) and Reddo has an interesting story about the FE van he used to have with a similar dilemma.
RTA says that although it looks like a duck and quacks like a duck its a penguin
Terry.
I can't think what to write here so this will do.