The article is old and while it contains some true facts it is quite weak in the arguments it makes. Recently the Gateway Development Corporation released a set of "mythbusters" that reveal that most of the typical complaints to be unreasonable. You can read those here http://www.gatewayprogram.org/content/d ... chment.pdf
. The writer has no understanding that a four track bridge is quite difficult to build and that such bridges are rare for a reason, most of the time there are two two-track bridges next to each other. He also does not get the fact that four tracks over the river do not resolve the problem that there are only two tracks east and west of the bridge(s). It is also incorrect that the bridge does not open. It does and there is already an agreement with the Coast Guard for openings to not happen during rush hour. The problem really is that when the bridge opens outside of rush hour and gets stuck it takes hours to fix and the delays spill over into rush hour.
If the railroad was private, they could try to buy out the one-two barge customers up the river and be done with that, but the state (or Amtrak as a state entity) cannot really do that. Even then the Coast Guard is unlikely to allow welding the existing bridge in place. For example, while there has been no river traffic up the Passaic River for decades, the Newark Drawbridge on the Morris&Essex line is still required to be movable.
The one fact from the article that is unfortunately true is the requirement for 10% capacity increase for the federal funding. They are trying to fudge this by using an old baseline with fewer MLV cars, and that is likely to end up being the reason why the Trump Administration will deny the funds. While it is true that with a fixed bridge they might claim capacity increase through the higher seeds allowed on the new bridge and as a result more trains, the capacity is constrained east and west of the bridge and that will not allow for the 10% increase to be realized by completing this project alone.