Actually, Inafune seems to be very biased toward SuperAdventure Rockman. Mandi of the Mega Man Home Page seems to have played it, and she kinda covers the thing ( link here: http://www.mmhp.net/GameHints/SuperA.html ).
The catastrophes Inafune mention all seem to be GAME OVER ENDINGS, and not simple, random story scenes. Either the military copters going down and the people dying were well-hidden story scenes, or the claim was blown out of proportion and he never thought about PLAYING his "own creation"'s games. SHOCK! I'M DISAGREEING WITH THE DIRECTOR!