Huh, that's interesting. You're sure it's not just some Zeromus sprites that happen to fit together like that? I haven't really ever examined Z's image in depth, but I ask because 1) they appear tonbe part of his sprite sheet, and 2) from what I can tell, it's a 2x4 monster, and I don't think the game has any of those by default (right?).
Barring that, I can't really conceive of what their plans might have been for this. I don't think Zeromus would ever have a good reason to hide in the ground. With the special BG during that battle, you'd likely not even be able to see most of "Baby Zeromus."
Anyway, cool find!