Sure, South Station has those amenities. But in my (very dated) experience, not nearly enough. A decade ago, when I used the station a lot more, I remember the few benches filled up quickly and lots of people standing, cramped waiting for a train. There was more seating with the restaurants but those would be closed off if you were there too early or too late. Bathrooms would have long lines out the door at certain times of day. I remember frequently sitting on the ground of the bus terminal waiting for a Greyhound or Chinatown bus. I don't have fond memories of the time I had to spend at South Station.
Others will know better if the situation has improved. But with all the plans for increased train/bus capacity, I wish there was also plans to account for the greater numbers of people going through.