1. I put grease (unaware it was not recommended). I have had no problems whatsoever.
2. You have two ways of bedding in the pads. First remember that the goal is to layer an even coat of pad material on the rotor. As long as the rotor is not evenly covered, it is at risk of being "printed" with pad marks that eventually develop into pulsating brakes.
So 2 approches, one where you let time fix the issue, and avoid braking hard (because that would mark the pad if not done properly), one where you face the issue immediately, do hard braking under controlled conditions and get it done immediately (but if you screw up, it will mark the rotors - I guess BMW has seen enough customer screw up to think it is better to just let them drive w/o hard braking).