Right now there are punitive speed restrictions throughout the system at all of these old bridges being targeted for replacement. The bridge replacements lift all those restrictions to near-track speed through those areas, in some cases doubling the speed. All that is collectively worth a bunch of minutes in time reductions to Amtrak schedules, and less commuter interference in Metro-North territory where it's a very intricate procession of trains due to overall congestion. Additionally, there is wide schedule uncertainty because of meets/overtakes at some of these bridge bottlenecks, leading to large amounts of contingency padding on the Amtrak schedules. Fix the bottlenecks, and you strip out the schedule padding leading to a bunch more minutes in savings. To the point where you're talking double-digit minutes just for the bridges. Finally, you've got capacity chokes at the bridges that open the most...like Connecticut River and Walk. Replacing those spans with much faster-moving lifts and modern bascules pries open a few more slots outright. So does quadding up 2-track spans like Bush and Gunpowder. And obviously Gateway doubles the capacity of the big Penn Station bottleneck, which will allow more NYC-terminating trains to be extended to Boston and Springfield and much better behavior intermixing terminating NJ Transit, LIRR, and (future) Metro-North commuter trains with thru Amtrak trains. Beyond that you've also got a bunch of general state-of-repair items to tackle, especially on the New Haven Line and Philly-Maryland which will improve overall reliability and allow for a few more minutes of contingency padding to get stripped out of the schedules.
But beyond CT River Bridge, the New Haven-Boston Shoreline route is at full state-of-repair and full speed for its geometry. All of the other movable bridges are modern 1980's-2000's spans in good condition with no speed restrictions. So there's no more time savings to be realized for Northeast Regionals east of New Haven after the CT River Bridge improvements get done, and no more time savings to be realized for the Acela after the Acela 2 fleet uprates the 150 MPH territories in Rhode Island and Massachusetts to 160 MPH. So that's why there were no Massachusetts- or Rhode Island-specific projects in this grand funding dump. The remaining list of capacity tweaks on the Shoreline are all about better meets/overtakes with commuter traffic, and that's entirely dependent on the future trajectories of (1) MBTA Regional Rail, (2) Shore Line East frequency expansion and extension to Westerly, and (3) buildout of Rhode Island intrastate Commuter Rail. There's no funding for those items yet because CT/MA/RI have not fully committed to those commuter upgrades and the new meets/overtakes that they'll create. So for now there's nothing really for Amtrak to do up in this area except study the bucket list of future intercity vs. commuter capacity upgrades (which they're doing), and be ready to pounce when the states fully commit to those commuter rail expansions.