Those deep caverns seem like a waste of an awful lot of money, considering two facts. First of all, Penn Station track capacity is not quite maxed out, the real problem is getting the trains under the Hudson, which could be fixed by building even a single track new tunnel. The trains could use some of the existing 21 tracks. A big win would come from the fact that if the new tunnel is built south of the existing one, the incoming NJT trains going to tracks 1-4 wouldn't have to intersect the Empire line, and for that matter would have significantly fewer crossovers to take. If they also build tail tracks past the end of the station, they get some extra space to store their trains, and if they run it like a subway, with separate relay drivers to pull the trains in and out of the tail tracks, they can turn probably 24 trains an hour on those four tracks. The problem then becomes one of how to get all the people on and off those trains fast enough, which is already partly solved by the new NJT concourse, and would be made even better with more stairways to access those tracks. And no need to build hugely expensive underground caverns. Plus, if NJT tries hard enough to encourage a reverse commute, they don't even have to take up valuable East River tunnel slots to take the empty trains to Sunnyside, since they'll be going to back to Jersey, and full of paying passengers.