Detective Barricade:
It's still a bit of an odd the way they worded it. Also note Mewtwo's Pokedex entries in the original Gen I games:
To me that sounds like the took Mew's newborn and experimented on it. Gen II makes no mention of Mewtwo's creation (besides Crystal saying it was "created solely for battling"). However Gen III had some oddities with its Mewtwo dex descriptions. RSE and LeafGreen stuck with the gene splicing and DNA manipulation story, but FireRed had a new dex description:
FireRed is the first to pretty much say Mewtwo was made from Mew's genes. Not admittedly the other dex entries are ambiguous about exactly what kind if gene slicing and DNA experiments went on. They could have experimented on a newborn Mew/Mew Egg or they could be messing around Mew's genes. However a thing to note about FireRed's dex entry specifically mentioning the recombining is that most of Mewtwo's future dex entries talking about its creation mention it was made from recombining Mew's genes and nothing on the gene splicing and DNA manipulation (except for those entries which were copy & pasted from old dex entries like X's and ORAS).
Also, the dub of Origins changed the wording of the Pokemon Mansion journal entries (the Japanese kept them the same):
The dub made it more clear Mewtwo was created and not born from Mew. Actually, rereading it makes it sound like the scientists impregnated Mew, ew.
Mewtwo being a clone is the current canon, I don't think anyone is denying that. All I'm saying ORIGINALLY it sounded like maybe they had another idea for Mewtwo's creation, maybe even going along the lines of how actual cloning is done (FUN FACT: Originally there was going to be a Pokemon based on Dolly the clone sheep, however they felt that would be too controversial. Dolly was created by taking an egg from one sheep, a mammary gland cell from a second sheep, and carried to term by a third sheep. So while they scrapped the Dolly Pokemon, they could have possibly kept the real cloning process and quietly recycled it as Mewtwo's original origin).
Anyway, as for Cubone, maybe there could be a bit of truth to its Dex description. Maybe while not directly its mother's skull and femur, a newborn Cubone skull and bone club maybe are external skeleton which shape matches that of its mother's skull and femur. As for Cubone's mother dying, maybe
WaffleTitan has an idea that for some Pokemon they can give live birth. Pokemon Eggs always seemed a bit... artificial, at least the Eggs that we know. Maybe people found a way to artificially stimulate a Pokemon to reproduce that is not the natural way they reproduce. Pokemon in the wild would still mostly need to rely on their natural reproduction methods and maybe its those Marowak who die upon giving live birth and Cubone mourning their deaths.
Possibly, also it could be the way Legendaries breed can't be done artificially or they just outright refuse to breed in captivity. Many Legendaries are also long living, they don't really need to breed that often, maybe once every century just to have a backup just in case something happens to them and they need to be replaced.
Hmm, are we sure the "Manaphy Egg" us an Egg? It doesn't look like a normal Egg, and when bred in captivity they produce normal Eggs that create Phione.