@Raving: Of course. Ninja is Rogue, just a Rogue that has more complicated changes than a simple archetype would warrant. This is also why both Samurai and Cavaliers can choose any order; there are no "Cavalier only" or "Samurai only" orders. They have no archetypes that they can share because no Cavalier archetypes replace abilities that Samurai still have and vice versa. Anti-Paladin is also an alternate class, but Paladin archetypes, again, don't have any replacements for abilities that Anti-Paladins retain (iirc. APs have no abilities in common with Paladins; just related mechanics). This is also why, if you have levels in Rogue, for example, you cannot ever take levels in Ninja. It would be equivalent to taking 1 level in Two-Weapon Warrior fighter, and then 1 level of Brawler Fighter to be a Fighter 1/Fighter 1 using two otherwise incompatible archetypes.
So if there is an ACG class that has the same class abilities as one of their constituent class alternates, and those abilities are changed by an archetype, by the principal of mechanical parity, they are entitled to choose that archetype.