VED relief is irrelevant to this discussion - anyone who gets PIP HRM will qualify for zero rated VED, regardless of whether they get their car through Motability or privately.
VAT relief is more complicated. Some people who get a Motability car would qualify for that if they bought privately, but not everyone. For a private buyer, you have to be a full time wheelchair user AND require significant (and permanent) modifications to the car. When Motability started, I suspect that a large proportion, probably a significant majority, of users qualified for this. However, as the criteria for claiming PIP has widened, the proportion who would qualify for VAT relief outwith Motability, has reduced.
I agree that there is a case for ending the blanket VAT relief for Motability cars, so long as it can be maintained for those people who qualify for it, in their own right.