Mark-ups make sense right now - each dealer has only a couple of these cars and that's all they're getting for a month or so. If these cars were all listed at sticker then they'd be gone now. As others pointed out, they want to sell the car, but since there's a lot of interest now and they still don't have a lot of them, so dealers have nothing to lose by marking it up now and seeing if anyone bites. If not, they can just lower the price in the next couple weeks and will still move the cars easily before the next batch rolls in.
Also, you have to consider the local markets - LA is expensive relative to the rest of the country and people do have more money (at least the people that can afford M3's do). I noticed that the dealerships with no mark-up haven't been in CA.
I went to the dealership in Glendale, CA and they wanted $20k over. Alexander first said $20k then they were willing to take $10k the next day. This number will go down the more people like me walk into dealerships and walk out laughing. 90k is def getting close to Carrera territory (though, fyi to those that have mentioned it, I was just looking at the 4S the other day and they're hard to find for less than $105k).