I don't think it's meant to be like that in the games. Cubone is its own species and evolves into Marowak. The reason it wears a skull as a helmet is a bit puzzling (not to mention grotesque) but either it's just a rumor (even in-game) that it wears the skull of its deceased mother, or its parent somehow dies before a Cubone baby grows up and ventures out into the wild. Thus, you never see Cubone without a skull helmet.
I think it's strange that Kangaskhan never got an official baby prevo - it even has one in its pouch! But it hasn't been given a name, just "Kangaskhan baby". There are similarities between it and Cubone but as it is now, the two are not related. It's fun to theorize though.
Also, there are creepypasta about it. But that's not official.