Stock profile (particularly around the comb nose) is certainly the biggest and most obvious one, but there are other things too, like; cheek rests, BP's, TG's, PB's, MC's, pipes, inlays, triggers, locks and side plates that contribute to each style being a little different, Of course, then you can get in to carving and engraving styles too.
The concept of different "schools" is a more modern one on an attempt to classify various styles by geographic region as to the makers. I doubt it existed very much in the day, but rather more by the individual maker(s) and their name and reputation. People didn't travel as much then as they do now, so if you lived in Lancaster County, and you bought a gun there, you likely got a gun that looked similar to those made there, which might be significantly different than one made in rather nearby Berks County for instance.
There were literally hundreds of makers operating in all these counties. In Lehigh County alone they seem to have documented up to 150 different gun makers and shops.