Well, since it now has a Mega evolution with the Dragon type, it's not really a problem any more. But its possible for a Pokemon to be related to other Pokemon of another type anyway. Types must change sometimes due to mutations.
Well, no, I don't buy that theory lol... It's well thought out, sure. But I think it's really simple. The legend that Cubone wears the skull of its dead mother is just a legend. The skull is just a part of its body. The Pokedex is chock full of unreliable folklore.
Gyrados is as much dragon type as Charizard. It comes from the legend of carp that leap over the rainbow to become a dragon. the only reason its not a dragon type in game is because water/dragon was way too OP in gen 1
Axew certainly belongs here, yes. Personally I think Gible should be related to Sharpedo, but not many people have agreed with me so it will probably end up in this tree too. We have more up to date versions of the reptilian tree if you are interested in seeing them.