Yes, the center speaker shouldn't be recessed on the rack so that the sound is diffracted by the front edge of the rack. Position it at least flush with the front edge. It isn't critical to have the center and mains the same distance away since receivers adjust the delay to compensate for a difference. The YPAO on the 3800 will do this automatically during calibration.
Toe-in is angling the speakers inward toward the listener. The Axioms have very wide and smooth horizontal dispersion when oriented vertically, but the best sound is still directly on axis, so the M22s should be toed-in so that the tweeters point at your ears. In general, the mains should be separated by about as much as your distance from them.
