I've never swapped wheel sizes on a bike before and I'd never thought about it before, but your observations make sense. The 21" front wheel has a larger moment (torque) to apply against the moment caused by the brake/rotor.
I paid close attention to the brakes on the motard track last night and again today commuting. I think they could be better. I don't find them a problem because with the little bike I don't use them to scrub much speed (it's all about maintaining momentum) and they are adequate for emergency braking. I do think that in some situations the modulation could be a bit better yet though. A few times last night on the track (same spot each time) I noticed that I reached a point where there was an abrupt change between off and on. It's a little unsettling, but can be managed. I may try a steel line yet ...
Overall I still won't complain about the little bugger. Next to my Ducati it's the best 'out-of-the-box' bike I've been on.