On the NEC, the gap between Amfleet cars and the station is nil. Yet Brightline's high platform station have a signifcant gap with the Brightline cars, and the cars have platform that extend, why? Surely the specs were known before construction of trains and station.
Loading gauge for many freight cars is larger than loading gauge for passenger cars. FEC operates said large freight cars. Such freight cars are forbidden on the NEC, so they can build platforms right up to the train.
Gauntlet tracks are another common solution to this problem. See: Raritan Line (NJT), SMART (Bay Area).
This question would be better directed to the FEC forum.