The reason why Springtrap and Scraptrap are different is because Afton was using remnant to make himself human, and the Scraptrap suits body was shaped more like a human body. This would explain why Scraptraps corpse looks different and has more organs. If we look at Springtraps corpse head, we see no ears or lips, so clearly Cawthon knows what a skull looks like. Scraptrap's corpse head was meant to be like a face, not a skull.
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