Danny Boyle discusses the character (andand visualisation) of Pinbacker at great length in this interview with TwitchFilm and this interview with BlackFilm.
My apologies if these two interviews seem very similar (he's clearly memorised his 'talking points''talking points') but both quotes shed light on the different aspects of your questions.
Why did he flicker?
It's not so much what is Pinbacker—obviously he represents fundamentalism—but it's really a challenge to [Capa's] sanity, which is of course what it would be to go out there
Why we visualized him like that is because of what I said before about witnessing. It's very difficult to say when somebody has lived out there for that long, it's not possible but who knows what's possible? We've discovered extraordinary things. So I wanted him to be spectral, but not like a ghost. He's literally like the bits that make him up—the protons and neutrons that make us all up—have kind of reorganized in some way.
Did he have superpowers?
Q : Why did you add in the radiation-scarred insane mad-killer Pinbacker character?
DB: It's introducing him into an otherwise realistically based film. Otherwise, it's an extreme psychological element, really. In a way, he's a character. He's based on the guy who piloted the first ship, who has had this transformation....
You have to represent that in some way, and we represented that with Pinbacker, this guardian of the gates of heaven or hell, whatever you want to call it. He stands there as a guardian at the gateway. I wanted to depict him in a way that was as extreme as I could do, which I could do technically, which is this blurring, this stretching. You take that kind of risk with somebody. I wanted him to feel that, literally, the protons and neutrons that make him up had been reorganized somehow--that he was no longer recognizable as a human, except that he is still speaking with a human voice and he is captain of the first ship.