I wonder whether Yglesias posted that observation about Penn with some fear that Amtrak would lock down the process and thereby kill the golden goose. It’s been several years now, and the enjoyable hack is still there, so perhaps there’s nothing to worry about.
I say the following with similar trepidation: if you want to avoid the incredibly stupid and pointless lines at South Station, just get on one stop farther along toward New York, at Back Bay; problem solved. There are no waiting lines, and people board trains the way they should — the same way they board subways.
Also, it looks like Amtrak is considering making the train system worse. Read this whole thread by a fellow whose Twitter description says that he is “Prone to live-tweeting transit plans.”