After wrapping up that challenge last night and talking about it now, something about one of the characters just dawned on me... Skull Face, is he Colonel Volgin?
Volgin got pretty messed up in MGS3 which would explain the face, and the voice just registered in my head that it's either identical, or at least pretty close to Volgin's.
It would also make sense because he would hate both Snake and Zero (Cipher).