I think you are wrong about the magnesium head transferring heat better than the alloy head, if you look on the os site at the v spec with the alloy head it says the the alloy transfers heat better than magnesium.
Wayne Walker from Australia who is a Mugen factory driver has been running the ninja MRT engines both on and off road for the last 9 months and has replaced all magnesium heads with the latest MRT alloy heads. Mugen sent new alloy heads to the Australian distributor for all MRT motors sold, why would they do that if there was no problem.
Wayne won the New Zealand Nationals running a Ninja MRT with the new alloy head where all other drivers running MRT's still had the magnesium heads and most had tuning problems because the engines run to hot. I hope this helps with your decission.
Barry Walker