Yeah, I could see this becoming a problem in the future. Imagine getting used to this, then for some reason, needing to drive an older car. "Oops, I didn't realize this car required manual braking".
There could be two classes of license, like in Japan where you can have a limited qualification to drive only automatics, or a full license including manuals too. In this case, however, the "automatic" would be the fully automated vehicle, and the "manual" would be the traditional human-controlled one.
The real reason for drivers licenses is social control. My father's first driver's license was never supposed to expire, my State ID was never supposed to expire, in both they changed the rules, and forced stores and banks to no longer accept "expired" IDs as proof of identity. It's not like your identity or age or ability to drive or anything else changes when your ID expires, they just want to keep you on their chain.
