Watching this evolve from a reasonably forward-looking proposal for four tracks with sufficient clearance for double-stack freight trains
I think there as a certain amount of community opposition to having double stack container trains running on Amtrak tracks. Given how double stack trains mess up passenger service out west, I, too, would be reluctant to have them clutter up the tracks of the Northeast Corridor, especially given the plans for more frequent passenger service. In fact, I'm not sure how NS freight service works in the Baltimore area, as they have a reasonably large yard northeast of the city, but the nearest tracks that NS controls are either north of Perryville or south of Washington. Maybe it's mostly coal trains coming down from the Port Road and then to the harbor, where the coal gets loaded on ships for export.
Also, there's a certain amount of ignorance among the public. I attended a public meeting a few years ago where some local activists went ballistic about the prospect of tanker trains full of Bakken oil going through the new tunnels. I think they called them "bomb trains" or something like that. This was some time when the Lac Megantic disaster was still fresh. I think the real issue was the possibility of tanker trains going through the Howard Street Tunnel, which may actually be worse, but that's actually the main rail freight route for the east coast, so there's really no alternative. Clearly, what they need to do is built a completely new freight rail bypass around Baltimore, probably running through the industrial area around the port, but doing that would not only require building a new harbor crossing, either a high-level bridge or tunnel. Somehow, I don't think CSX or NS would find it profitable to use their capital to finance this, and public financing would be another "internal improvement" controversy about taxpayer money from the many providing a benefit for the few (CSX or NS).