I know that in MML2 they tell the story of how the Megamen included have the ability to turn themselves into Carbon based lifeforms
...what in the blue hell are you talking about? The only other character with the title "MegaMan" in the Legends series is Juno, from L1, and neither he nor Trigger are seen to transform (although Juno plugs himself into a second body, his actual form does not change).
I'm guessing I'd better start from the beginning here. "Carbons" in Legends is what the people of Elysium call the people of Terra (Earth). The entire population of the planet was in fact artificially created, they themselves just don't know it. Trigger is not a Carbon but is similar enough to them that he passes for one, to the point where neither he nor his adopted family notice anything odd beyond his understanding ancient languages (which he takes notice of in L1 upon opening the Main Gate). He was found as a baby by Barrel, and he is seen in L2's opening wearing normal clothes, so yes the armor is just armor.
Trigger is one of Elysium's people, more specifically a Purifier Unit (their equivalent to a Maverick Hunter). In asking whether or not Trigger is a robot, you kind of need to define the term "robot", since the last known "true human" (according to Sera) is the Master whom Trigger previously served, and he died long before Trigger was "reset", sealed, and found by Barrel. Humanity in Legends is extinct. Trigger is artificial, but is no more so than anyone else in the series.