I've only gotten the first ending and I took what happened to mean that since I didn't get all the cubes (something like 34, instead of 64) the restoration of the big God Cube didn't work. And Gomez (and presumably the rest of the universe) died. Hence all the metaphysical inexplicable pixel stuff. Gomez bangin' the drums was something that happened in his afterlife.
I thought this was vaguely hinted at in the achievement, as well: as it's called "Kill Screen" - both a reference to the last screen of old arcade cabinets and Gomez's fate the first time through.
I haven't gotten the second (or third! If it exists) ending though, so maybe I'm way off.