Travis Young 302's page

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Alternate Classes from Ulimate Combat, Page 8
"These are standalone classes whose basic ideas are very
close to established base classes, yet whose required
alterations would be too expansive for an archetype. In
this case, that’s the samurai and the ninja—specifically
Asian-themed classes that have long and unique histories,
as well as great cultural cachet, but which are similar in
concept to the established cavalier and rogue, respectively.
An alternate class operates exactly as a base class, save
that a character who takes a level in an alternate class
can never take a level in its associated class—a samurai
cannot also be a cavalier, and vice versa. The antipaladin
from Advanced Player’s Guide is also an alternate class."

I'd read that to be you can still play an archtype, as long as that archtype replaces things that haven't already been replaced. (Much like you can have two archtypes, as long as they don't overlap)

So I don't see any problem playing a scout ninja, as the ninja gets uncanny dodge, and imp uncanny dodge.