It doesn't matter what Musk does with the methane, what matters is that he's at best exploiting loopholes and at worst operating extrajudicially.
Also, SpaceX "powering the human colonization of Mars" is a pretty huge sip of the Kool Aid there. Given the founder's track record, it's about as believable as "fully self-driving cars in a year".
But, more importantly, it's irrelevant to the problem at hand, sidestepping the regulation process