No, it never actually goes into the pentagonal show building as per those leaked plans. It does run below the queue though, the turquoise structure I had highlighted.
This one demonstrates what the second floor looks like:
My completely (again educated) assumption is that the actual boat ride in the leaked plans was just a rough placeholder at the time to demonstrate how the Flight of Passage queue would eventually sit on top of a small chunk of Na'vi River Journey. Which is also why I don't lend too much credence to the plans naming it a C-ticket. That leak occurred well before Cameron was happy and one of those compromises likely involved plussing the C-ticket boat attraction it references.