| Chess Pwn |
for PFS it could also be that Ninja has no racial FCB options.
EDIT:
Alternate classes never say what they are or how they compare with their foundation class other than saying you can multiclass the two. They never say that a ninja counts as a rogue for stuff, never say it's able to take rogue archetypes or FCB. And it has been said that Alternate Classes are just big archetypes, but that has been "officially" said to have been incorrect.
We currently have nothing official about Alternate classes, so now the general view that you can take rogue option has nothing to support it and someone saying you can't has rule support. We're not likely to get a FAQ because enough people don't care because they feel it's okay. I believe this thread is the leading FAQ count if someone wants to add their support to it.