It's a spin off, it doesn't have to stick to the original stuff so strictly, it's an alternate timeline post MegaMan1 if you want to look at it that way. Anyway, on a side note, take a look at this:
http://www.youtube.com/watch?v=qfVPyTjrhPQ <-- skip to 1:17
In this official MegaMan game "Super Adventure Rockman", the six masters ARE in Dr.Light's control again and they even help MegaMan. I know Dr.Wily used them against MegaMan again in The Power Fighters games, perhaps he re-reprogrammed them? It always has been unclear what happens to most Robot Masters after they're defeated in the official storyline :p
http://www.youtube.com/watch?v=qfVPyTjrhPQ <-- skip to 1:17
In this official MegaMan game "Super Adventure Rockman", the six masters ARE in Dr.Light's control again and they even help MegaMan. I know Dr.Wily used them against MegaMan again in The Power Fighters games, perhaps he re-reprogrammed them? It always has been unclear what happens to most Robot Masters after they're defeated in the official storyline :p