Tankbuster,
FYI, i asked this same question, FWIW, see the thread at
http://forum.free-track.net/index.php?showtopic=573. I gather from that info that the software's mathematical model assumes that the top led is further away from the camera, and the two side LEDs are closer. FT doesn't let you enter a negative value. I think having the top center LED closer would confuse the program, that was my experience.
Also, it sounds like there is good reason to keep it that way. The two LEDs to the sides obviously transmit twice as much motion information as the one top led. But if the side LEDs were further away from the camera, they'd be closer to a center of rotation, meaning they'd be moving less when your head rotates on one axis since they are near the center of rotation on that axis, hence negating the advantage of having two transmitters. In other words, the further from the center(s) of rotation the sensors are, the more accurate the tracking, though other things come to play- you only have a finite amount of space to be in the camera frame for example..
Feel free to correct me if i'm wrong.
Robert T.