Most transmissions lose to a manual. So what? The efficiency of the whole system is what matters.
Not all automatic transmissions lose to a manual. However, conventional automatics do, I'm not arguing that.
As for computer operated manual with dry clutches, that's a different case, and probably something where these big BMWs (which you compared to) have upper hand to Prius' transmission. For example, the M5. Their engine isn't, but that's besides this point.
Besides: I can't imagine the system is particularly inefficient. It's a planetary gear setup with no shifting gear ratios, no clutch, and no torque converter.
However, the belt itself is what causes the inefficiency. It's flexibility and slipping causes the power to get wasted as heat. And this number is a lot higher than what a cluth slips.
Competence, like truth, beauty, and contact lenses, is in the eye of the beholder. -- Dr. Laurence J. Peter