I can't really speak for Phil, but I have a feeling that, in this case, he'll still be keeping the name Nitro Man. The title of our game was one thing, it NEEDED to be changed, but as for the name of his robot master... I know that Phil designed Nitro Man when he was just a kid and that the robot master is dear to his heart. I don't think this is going to make him change it just because an official game has the same name.
Therein lies the inherent problem: People will get confused.
Fan #1: Hey, have you seen Nitro Man? He's so cool!
Fan #2: Yeah, he blows up stuff and ain't afraid of anything.
Fan #1: Not
that Nitro Man, the other one!
Also, consider the recent "MM10" assets debacle...If Capcom learns that his RM has the same name as theirs, he might get sued (although, how likely this is, I have no clue). Getting his game confused with theirs is bad enough...
I think "Trinitro Man" would be fine as a substitute name, just in case. When making MM fan games, one has to be ready for any eventuality.
Edit: At any rate, we'll see what MPX will do (if he does go on the net today, that is).