Just because the timetable says it stops there, doesn't mean you can get off the train there. For example, if someone departing GCT on a New Haven line train has a ticket for Fordham, the conductor will extend the ticket to Mount Vernon East because that's the first stop the train will discharge passengers at.
It's not up to the engineer (there are no T/O's employed with Metro North) to decide to skip stations just because there doesn't appear to be any passengers at these stops. Passengers could be hiding in stairwells or shelters waiting for the train to come through.
Generally speaking, should one want to travel from GCT to 125 for Fordam, per the timetables, it's Harlem or Hudson line locals that discharge passengers at these stops. The same holds true for those traveling from Fordham or 125 to GCT.