I have the PFC BBK, front and rear, and have had no rotor fitment issues nor do I have a vibration/unbalance due to the rotors.
I'm guessing the designs of the mounting hats are different between the stock and BBK rotors due to rotor thickness and/or caliper placement but they had to be designed using the same measurements taken from James' stock e92 M3. The current issue of GRM has a brake pad comparison test and they used PFC rotors for all pads, and if James thought there was a safety issue with the basic design I doubt he'd be heading into the turn 1 braking zone at VIR > 150 mph as well as using them on the GS race cars. I could be wrong but I believe Ganassi Racing uses the same design on their DP race cars.
For people considering the PFC BBK...Compared to the AP Racing BBK on my e46 M3, the PFC calipers have better initial bite/release characteristics and modulation. I've never driven an e9x M3 with APs calipers so I can't make a direct comparison. However, comparing the two setups I'd have to say overall braking performance is very similar (no fade, no soft pedal under extreme conditions) and given the extra weight of the e92 M3 (plus my e46 is not at stock weight) that's impressive - if I had to do it all over again I'd still go with PFC. Feel free to PM me if you have any other questions.