Silent Hill 2 is my favourite game of all time, so my theory goes as follows.
All the enemies in Silent Hill 2 are female, as James's psychological issues all stem from his life with and subsequent murder of his wife. Pyramid head is the one male creature, and is obviously phallic in appearence, and goes around mutilating female monsters. Pyramid Head is James, as he sees himself.
When he is forced to confront Pyramid Head, he is invincible and James is helpless because James has not yet come to terms with his actions. By the end of the game he has, and he understands what he has done, and Pyramid Head destroys himself.
His appearence in homecoming is kinda just for the fans. The protagonist has a similar fear, that of an overpowering childhood 'Bogeyman', that haunts him. It just happens to look like Pyramid head, is all.
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