You would hope that at the end of a lease, if asking for a price to buy the car, Motability don’t inflate the price they offer it at because of the premium paint and/or any added options the customer has already paid for at the outset!
At the end of the lease Motability will value the car and sell it for the best price they can. So colour trim and extras will make the car more valuable. If you go back to the 80’s standard trims, the L , GL and GLX, if the L had no AP and you went for a GLX, you paid the higher AP to cover the higher cost, but at the end of the lease Motability obviously could ask for more back for a GLX over a L model. Also the less millage and arguably the less use you get out of your car the more Motability will value that car at and ask you for a higher forecourt price for it. This obviously is a contributory reason why Motability makes over 1 million a year in profit and are sitting with over 1 Billion in the bank.
The appearance including paint colour and condition will also add to the value of the car. Originally the Motability customer had to pay more if they wanted Metalic paint, then Motability realised that the metallic painted cars were holding their value more as they (to most) looked better and so they stopped charging extra for metallic paint and only charged the extra difference for Premium paints. Now going by other Motability sites, people to some extent seem be to be paying extra depending on Makes and Dealerships.