In a computer setup, where speakers are placed a good distance (a few feet) behind the location of the screen what is more important to good sound:
1) A center speaker that is at the right height with respect to the left and right speakers, but is occluded by the screen. Remember that this is an LCD monitor, not a projection sheet.
2) A center speaker that has an unoccluded path to the listener, but is not at the same height as the mains, though angled down.
Perhaps a better way of asking this is can Audyssey effectively deal with the sound change that you'll get from having a speaker that is occluded by a solid object?
You will get much better results by placing the speaker above the LCD monitor and tilting it down so it points to the listener. Putting it behind the screen will affect the high frequencies so much that it will not be possible for MultEQ to correct for that effectively. The compromise with not having all three speakers at the same height is that sounds that are designed to pan across the front will go up in the middle. But, I think that's a better compromise than having the muffled sound of a speaker behind the screen.