Perhaps it's the case that the skull around Cubone's head FORMS into the shape of its mother's internal skull?
Like, through genetic memory or some other handwave shenanigans that will leave whatever bright mind that coined it spinning in their grave like Charles Darwin?
There is a theory that cubone is a baby Kangaskhan and the skull was its mother's, but with eggs nowadays its pretty much discredited at least in terms of gameplay mechanics
It's more like the Gen 1 pokemon weren't intended for genders or eggs to start with. (Hence why you have Nidoran boys and girls as separate pokemon types, the only pokemon where gender is a separate species without really having much to differentiate themselves the way that Tauros and Milktank might hypothetically be the same species, and yet are obviously wildly sexually dimorphic.)
Granted, even in later gens, there are breedable pokemon like ghost types that are supposed to be the ghosts of long-dead human Pharaohs that give birth to more entombed human's ghosts.
Ah! The egg finally hatched!Lies!!!If you are my mom, I would be wearing you on my head!Stop cracking jokes!
That thing you were wearing ever since being born can't be your mom!Then what am I!?Geez. All this boy does is read books. He has turned into a stubborn blockhead!knockEncyclopediaSonny, I'm your mother!Cubone vs MarowakWhy don't you see the real thing for a change!?Uwahhhh! That hurts momma!