First of all, the Park Avenue Viaduct, which was rebuilt in the last 10 years, used to regularly handle long haul trains which were normally well over 10 cars long and those cars were much heavier than the current Shoreliner cars. As far as station lengths, what is done on stations which can't handle more than 2 or 4 cars on say the lower Harlem, ie Tremont, Melrose, Woodlawn, Williamsbridge and Wakefield? Passengers are told that only the front or rear 2 or 4 cars will open at one of the aforementioned stations. The same could be done at the stations above Croton-Harmon or North White Plains. Diesel hauled trains are usually packed with loads of standees. One or two additional cars could easily take care of that problem. The last thing a person who has just worked 8 hours in the city wants to do is stand up for an hour/hour and half to travel 50 to 80 miles home.
the park avenue viaduct still has same maximum axle load as before the rebuild and the genesis is past that maximum weight.
this reason a genesis can only be fueled to 2000 gallon despite the tanks being 2200 gallon.
any engine with higher axle loading would cause big problems.