Many things are VAT exempt. The VAT exemption on Motability vehicles isn’t an inherent part of the scheme, it’s because they are for disabled people. In the same way that home adaptations for disabilities are VAT exempt. Medical, surgical supplies, mobility aids, specialist equipment, vehicle adaptations - all VAT exempt for disabled people - which they have to prove btw.
Similar with the VED. Even if the disabled person didn’t have a Motability vehicle they would still be entitled to apply the VED exemption to another vehicle, because it is a disability ‘benefit’.
Both of these exemptions are to help make the scheme affordable to a larger number of disabled people. The average income of disabled people using the Motability scheme is half that of other UK average households, at around, £18,500.00. These are not households that would otherwise be buying a car through usual channels and therefore paying the VAT. It isn’t ’lost’ revenue, it is revenue that wouldn’t exist anyway. They simply wouldn’t be able to have a car. And when the car provided means they can stay in work (and, whisper it, pay tax) that undoubtedly saves the state money. A lot of it.