Why is that weird? The biggest train stations in the world are here in Tokyo, and they don't have any place to sit down either, except in restaurants that usually aren't close to the main pedestrian traffic going to/from the trains. The idea I guess is you're supposed to sit on the train, not in other places where you'll be in the way. If you're waiting a long time for the train, you've done something wrong.
Its been a few years since I've had to go through Penn Station directly other than for LIRR. As I recall from my NE Corridor commuting days the lounge requires an Amtrak ticket. The NJ Transit waiting area had no lounge and no seats meaning people would begin to bunch up on the stairs. Admittedly, it might have changed in the intervening years.