I don't think the goverment loses out twice.
From the Motabilty website:
The Motability Scheme enables disabled people to exchange either their Higher Rate Mobility Component of Disability Living Allowance or their War Pensioners' Mobility Supplement to obtain a new car, powered wheelchair or scooter.
Essentially, the scheme is a leasing scheme,and the leasing rates reflect the end value of the car.
also, the car doesn't have to be driven by the disabled person, just used for their benefit.
An aweful lot of the cars make a very good low mileage purchase at the end of the lease