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No its explicitly an archetype. Just a complicated one.
Incorrect, I'm afraid.
Ninja is an alternate class.
Rogue is a core class.
And there are also base classes.
Archetypes are defined as:
Archetypes are a quick and easy way to specialize characters of a given class, adding fun and flavorful new abilities to already established adventurers
If you haven't checked the links yet, an important point about alternate classes is this:
a character who takes a level in an alternate class can never take a level in its associated class
I realize where your argument is coming from, but archetype is a keyword with a very specific definition in the Pathfinder system.

Omnitricks |
Actually ninja is an alternate class for rogue. The question comes from seeing that in the respective talent/trick list there is at least one that allows the PC to take the talent/trick from the other class.
Now looking at the advanced/master talent/trick, ninjas are expressly stated being able to take advanced talents from the rogues but the rogue does not have the same for the ninja's master trick.
I guess its logical to ask the GM and it being likely and not unreasonable to have the rogue take master tricks but I was hoping to have something official to save time.