In that case the tweeter is being picked up by the mic from a direction that is incorrect. It's not the end of the world, but the highs from that channel might be attenuated by Audyssey more than it should. Try it and listen for any negative effects from the non-standard incidence of the sound.
Beyond that, and I know the reasons for in-ceiling speakers, the sound from ceiling speakers is reaching the listeners from direction other than the intended one and the one "assumed" by the mix.
Edited by pepar - 1/16/13 at 8:55am