The older Ford escorts etc had the flap in the carpet, i would expect that it is normal to lift the flap to check the vin number.
They can't dismantle anything, but they can't fail something that they can't see (AFAIK) I'm sure it'll change at some stage. Some testers can be known to do what they want though
maybe the vin isn't legible?
56 350 2.2 130ps mk7 with 2 side doors
65 290 2.2 125ps custom with 2 side doors
07 350 170ps
Ids v86 licence + v86.04 update + xprog
hereIds map
here