Has apple now enabled FTS in the standard/built-in sqlite library?
This guy confirms your findings by asserting in his second blog update that FTS3 is included in iOS 5's SQLite library. (I have also tested this and came to the same conclusion.)
I have tested this on my machine and Lion OS and it worked perfectly, however build would not execute FTS on any other machine (all the queries would work except FTS). Same project built with Leopard OS would not result in usable FTS.
But dropping amalgamation source in project (and enabling FTS) results in amalgamation being built and running on any machine.