Second hand autos almost always sell for more than comparable second hand manual cars, not the other way around. In fact, in certain market segments the premium can be significant, as manuals become less and less desirable the further up the price range you go.
I would hazard a guess that the difference in price that Motability charge in AP for an auto over a manual (which is usually a lot less than the retail price difference) reflects the difference between the additional retail cost of an auto (less discount) minus the additional resale value that an auto would achieve at auction at end of lease.
I’ve always felt that the total costs (depreciation, running costs etc) for any car, whether that be manual, auto, EV, ICE, expensive or cheap, should be reflected in the AP and that no one type of car should be subsidised over another. However, given that Motability Operations make a sizeable profit out of each and every lease (around £500 from memory) and this is used to help pay for their over the top remuneration package (I’m not talking directors here, but ALL of their employees) and their whole purpose is to keep disabled people mobile, I find it disappointing that those whose disabilities mean that they can only drive an auto have to pay a premium. Motability could take a hit on the profit of those leases without needing other drivers to subsidise them. But, then again, Wigwam makes a fair point about auto not being the only essential requirement for those with certain disabilities, so where do you draw the line? The grants system exists, but always seems unfair to me as it’s means tested, unlike the scheme in general, but that’s a whole new (and very contentious) issue!