That citation doesn't actually address the question. The citation is that there's no such thing as an Unchained Ninja. The question was whether you could multiclass with levels in both Unchained Rogue and Ninja.
Now, I agree that you can't do that multiclass option, but I'm actually not sure why that's the case, since alternate classes are no longer considered extensive archetypes. (Which is why I looked at the citation -- I wanted to know how that worked now.)
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