According to SHS, the original SHS track uses a code 131 rail size that was chosen, "because it corresponds to a size of rail used on real railroads, yet still allows operation of AF and AF-compatible wheels." So it's supposed to be compatible, but there may have been some variety in flange sizes. I haven't gotten any of the MTH track to compare, but it should be the same rail size. Hopefully, someone who runs AF on SHS/MTH track now will chime in to give some first hand experience.
Mike A.