BMW is not going to design a completely new engine for a car with a one year production run. The 1M is a great exercise in seeing what they can do by swapping parts. A wonderful experiment so to speak.
I would suspect given the perfomance difference shown between the 1M and M3 (the 1M can be easily tuned to beat the M3 on the drag strip and on most race tracks) if they keep producing it (in the FXX bodies for example) they'll always end up using a "tuned" normal series motor so as to not surpass Big Brother. Would seem cheaper that way than building a seperate motor that will have to fit between the motor in the 1XX and the M3.
Just my thought anyway...