I'm sure if you did a change of particulars which was changing anything which would have affected VRT at first registration then you'd probably be liable for any extra VRT owed. I wonder are any of these discrepancies back handers or favours done so that VRT would be cheaper?

I know when I VRTed my e34 some years ago there was a difference of a few quid on the different drop downs. I went for the cheaper option at the time if I remember correctly. Now my e34 wasn't expensive to VRT but I'm sure there would be many cars where a dealer could make a saving by registering cars incorrectly.