So the penalty I'm calculating is the stop penalty of slowing from a cruising speed to a dead stop, waiting at the station, and then speeding back up to cruising speed versus maintaining cruising speed the entire distance; you can think of this as the time penalty that the Route 128 stop generates (being on a nice straight track that allows very high speed).

What you're talking about instead is the penalties imposed by a more constrained right-of-way in urban environments. Except when we're talking about Philadelphia (or most of the Northeast in general), you can't really escape from a constrained right-of-way anyways--a quick crayoning suggests you're adding about 20 miles of railway route which, even at 200mph, adds more time than you're saving by itself.

Consider again the cost of bypassing to save time. How many millions of dollars are you willing to save a minute of travel time? It is far cheaper to put that money into straightening the worst curves of legacy inner city track than to spend it bypassing the city altogether, not even accounting for the loss of revenue by not serving what are objectively large cities.