Sounds like a lose lose situation, surely the idea of basic training is to train you to ride a bike. As you said, in a car, auto test, auto license, manual test, manual license. I was worried about the possibility of doing my cbt on an auto, but my instructor agreed that it would be a waste of time, especially for someone like me who had never ridden a bike before, so i needed to learn how to ride a manual bike, which is surely one of the reasons behind a cbt! To learn! At the end of the day, your boy is the customer, if he wants to learn on a manual, then thats what he should do, even if he needs extra training.