I was told, via some folks who claimed to be Metro-North Railroad conductors, that there are no hard and fast rules re: seat checks; each person (or train crew) just does it his/their own way.

NYC-area commuter railroads have seat checks with a bunch of numbers on them, sometimes with letters. I figured that the letter indicated the direction of the trip and the number indicated the fare zone number, but in practice that's not necessarily how seat checks work.