If it is etched TM on the pick up cover, it's just TM for Trade Mark. There would be no difference in the actual pick ups.
Now, just to add confusion; there are 58/15 S pick ups that come in the SE and S2 guitars. Those are import pick ups. There was also the 58/15 MT, which stands for Multi Tap. Those were originally in the Cu22 Special Semi-Hollow Ltd. Those have the best tapped tones of any of PRS pick ups, with the exception of the pick ups in the Paul's Guitar and ME-V. I don't know that the MT made it to any other models, unless it was a Wood Library run spec'd by a dealer.