The Auburn Road and the Corning Branch crossed in Geneva. Both of them were fairly busy routes for NYC back in the day, so I can see why there was a tower there. Also. NYC and LV did interchange in Geneva... with LV sending their pick-up (local) into the NYC yard.
"It is highly likely that the 1990s were an overrated decade."
Just speculation, but NYC had "standard" plans for many of its structures. It's possible they just went with what was on the books.
Fallbrook was double track, Auburn Road kept passenger service until a fairly late date. Related question - did GY operate the switch from the Fallbrook to the Auburn Road at the west/south end of the yard? I would guess no due to the distance involved but would be interested to know. the guy who could have told me passed away last month.