According to the official databank, the deformation is purely because of lightning melting his face in the current canon, not an ulterior method. http://www.starwars.com/databank/palpatine-biography-gallery (The image with Palpatine’s “Unlimited Power” face has the caption you’re looking for)
That leaves the method by which Luke didn’t get deformed a mystery, but for that:
You’re all thinking too hard. By which I mean you’re trying to impose logic on GL’s prequel thought process. By which I mean you’re attributing a thought process to the making of the prequels.