Really, REALLY doubt that the "bad guy" was chosen to be like Einstein because of bomb stuff. America LOVES its military and wars, and every time someone says something about Japan, someone somewhere takes the convo to be about war, plus you always have tons of war stuff on TV and films etc. Japan is nothing like this at all. They're also not people to hold grudges either, especially about something already done and finished, especially when it doesn't even involve the people of today, especially those making these games.
I'd say it's highly likely that they did choose Edison and Einstein because they're very famous, so that works out. Then you have Einstein's hair, making him look more mad scientist like, sooooo, might as well make him the bad guy then!
I'm quite certain this train of thought is far more likely that what they suggest in the video. (And I actually find it quite silly and ignorant how you apply western, especially American thoughts to a completely different country. Just because your country is nuts over war, it doesn't mean the other has the same feelings/thinks about things the same way, although us humans tend to do this with everything when we're not careful.)
Anyway, good video :p