Nefreet
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Samurai, Ninja, and Anti-Paladin are just 20-level Archetypes for Cavalier, Rogue, and Paladin (respectively). Although this question has been asked several times, there is no debate about the answer.
This doesn't need to be FAQ'd. If you can find another Archetype that doesn't swap out any of the same class features (I'm unaware of any) then you can legally apply that Archetype to the Alternate class.