The logic in your example doesn't quite add up. Even if you try to bridge the gap and explain things, you're still stuck with dealing with the fundamental disconnect in that the games are split between Gen I-V being treated as self-contained stories vs. retconning in new information with each generation. But then again, we're talking about a series that doesn't care to put effort nor emphasis on explaining changes with each gen (at least not until the multiverse nonsense with regards to Mega-Evolution in ORAS).
I didn't say that the Dusk Stone is a Ghost-only stone, just that it gives Ghost Pokemon new ways to evolve, since logically speaking, you wouldn't expect a Ghost Pokemon to evolve with a Fire/Water/Leaf/etc. Stone, unless you intentionally built the Ghost Pokemon with the elements in mind. Though I should mention Dark types too as Honchkrow evolves as a result of the Dusk Stone, so that's two types that could use the Dusk Stone as logical means to evolve.