Amtrak's sitting area is distant from where they ask you to line up for the trains, which starts more than an hour before departure (like airport gate lice). It means you are forced to stand or forced to take really unhappy seat choices on the trains.

Airport gates have seating areas!

The problem is, it's now policy to not have benches in transportation facilities. They do not want to have to move homeless people off of them, because there are now tens of thousands of documented homeless people in the city every night & the shelters are terribly unsafe and overcrowded. So they've removed or altered benches in the subways, they close parks, they've taken benches off the sidewalks, and now they build new train stations (notably Moynihan and WTC) that have nowhere to sit at all, except for the tiny disconnected far-from-platforms Amtrak waiting area you mentioned.

People are mentioning it because sometimes they WOULD like to sit, and commuters are sometimes waiting 1-2 hours for their next train when it's off-peak service. (e.g. the weekend trains on Metro North past Croton and White Plains are hourly, and some destinations have even less frequent service) And these people tend to have luggage and don't want to arrive early and stand around with it. This isn't a bizarre hypothetical.

>now Penn is mostly serving commuters.

Go to Penn Station at about 9 pm tonight and you'll see those some of those commuters sitting on the floors as they wait almost an hour for the next train on their line.