Good question, Mist. I don't know much about the EU so I couldn't answer. My guess on the differences of this theory and the inhouse production work from LucasArts is merely coincidental, since they've never been alluded to before. Perhaps the EU work isn't restricted because it's not necessarily canon. That or these particular deformations are related to humanlike species and wouldn't affect some alien races, i.e. Maul. Although, I think the issue with Maul was more of inexperience than anything else.
Might sound like a cheap excuse, but then there's also the issue of midichlorian count/power. Even Maul had to train for some time, although I'm not sure how long his training was. Obviously, he was young and unable to use Force lightning. Possibly, it wasn't even possible due to his midichlorain count. And Dooku, with all his prior knowledge of the force, still had no degredation genetically after Dark Force training. As it was explained before, it could have been due to a political stance versus outright evil. Either way, his knowledge combined with exposure to the Force made it possible to weild force lightning. Although, the genetic repercussions were abated for one reason or another.
I think Palpy and Anakin represent hatred and evil in there "purest" forms. They were both raw power, with Anakin coming along with an even higher potential and midi-count. Hence, GL's comment that Anakin becomes pure evil. The two of them dominated a universe, a feat not referenced in any documentations of Star Wars history. None that I know of, at least.
A unique case, the two of them, but there are references that could link the midichlorian theory. All of the Sith have displayed either physical deformations (whether as mild as Anakin/Palpatine/Maul's eyes or as extreme as Palpy's face and Anakin's skin) or unatural force abilities, i.e. Dooku/Palpatine's force lightning.
Albeit that raises a question of Anakin's ability to use force lightning in the game. It could be creative freedom or a progressive based system, and all this might even have merit in the game.