I am not sure exactly how MFT is integrated into the stereo system, but I would imagine it is integrated fairly extensively due to the MFT voice and Sync features being played through the stereo. An aftermarket stereo would likely break this functionality.
It is indeed possible to retain all the key SYNC features. Check this out, as it was done years ago and possibly they will make one for the ST or Focus in general after 2010 since it is compatible with 2008-2010. This is the first site I'm sure if I put an effort into looking I could find something better.