Well seeing as how the final boss is Skrillex and you have to defeat him while he throws the corrupted cubes at you, I'd say yes they do represent his music, which is "corrupting the world".

It is tongue in cheek and that is part of the charm.

Totally. I saw it more as him having fun with his image than him being the butt of the jokes.

I think not. If it is making fun of him, it is doing so in Some way that required active participation by Skrillex himself, because...

WARNING, POTENTIAL SPOILER ALERT: If you beat the game you see a video clip of him that is specific to the game.