This is a great thread. I really enjoyed this first part of the season premiere.
I don't think Olivia is faking altLivia. The B-Lymphocytes definitely took over throughout her escape due to the adrenaline (examples: unreal memory, incredible marksmanship, plugging Frank in for Peter, the safe house/home address, the yellow paint). However, adrenaline wears off. The memory-swapping process is highly experimental. I think without it - even though she is now in a lag time when altLivia's memories have taken over - the "blood barrier" will break down and her original memories will trickle back. At this point, I think she may just play the game to see how the altFringeDiv team can help her get back.
As for our universe, I'm still working on the Peter deposition and the whole pen thing. (Will need to watch the ep yet another time.) I don't trust the interviewer at all - his questioning and attitude (but he's probably just an incidental character here). I think it is significant that Peter is dressed in lighter clothing (white with a touch of gray) than everyone else in the scene - both inside and on the steps. Savior? Shining beacon? More than human?
However, I don't think Peter will be the one to discover altLiva isn't his Olivia. It'll be Ella first (because kids are good at those things) > Rachel > Astrid > Broyles > Walter. It may be a while for Peter to come to grips with this.
On a side note, in watching the last few season 2 episodes and 3.01, I think that we'll gradually get a finer, complete view of Olivia. Right now we're up close, but I think this season will pull us back so we can see all the pieces that make up the talented Ms. Dunham.
OK, I'll shut up now.
And twiddle my thumbs until Thursday. Looking forward to part 2!