Warranties should remain intact, if the car is serviced by any VAT registered service centre and genuine parts are used.
This raises potential issues if you were to buy a nearly new car from the likes of Motorpoint and their service centre’s using after market parts, which can have serious implication further down the line, should one require warranty work or manufacturers goodwill gesture when out of warranty.
Motability are just penny pinching and will loose more in auction/resale value, than if they had paid for a 3 year sevice or got a service plan at the start. They own the car and their rules apply at the end of the day, but I won’t be loosing any sleep over it.