The article as is usual these days is poorly written.
The complaints are mostly about the short trench and cut and cover section where the alignment meets up with the NEC at its south/west end and the ventilation shat near that end. Notwithstanding all the description about the routing of the tunnel I doubt that anyone is complaining about the deep bored sections.. But then an article about four blocks would not be as eye catching as one talking about vast swaths, most of which is not really involved in the case.
The Baltimore Banner, where many of the Sun's journalists went, also has an article. The soft paywall gets you one article, use it wisely!
The median incomes over the new tunnel vary in patchwork ways but trend upward as you go east towards Penn Station.
https://www.city-data.com/income/income-Baltimore-Maryland.html The Banner article refers to the 2017 Record of Decision (FRA), the one with four tunnels and three ventilations. Do we have documents on the revised, electric-trains-only plan? My impression from the Banner was that the activists and NYU legal team are conflating 2017 with now, but maybe the writers got it wrong. Lawsuits are adverserial, and this sort of factual problem seems common in nimby vs. yimby situations. (Yimby websites enthuse over development, check out "Next Miami" sometime.)
Onward to my experience! I've visited Mt. Royal and the generally eastern half of the route a few times over the years, and it is one my favorite neighborhoods on the East Coast. Lots of trees, hills but easy enough to bike on, many streets divided by linear parks, two college campuses (MICA and UB), all south of Druid Hill Park. I got to see a nimby sign, next to a small gazebo on a former streetcar track. The median income map doesn't tell the full story. By contrast, the Trailways buses I used to take to NYC in the late 1970s and early 1980s detoured to the bus station from the I-95 on the far eastern side of Baltimore, through miles of formstone rowhouse blocks, far less leafy. That's the Baltimore you see in John Waters movies, or Hitchcock's
Marnie, with its own Charm City folkways (painted screen doors, etc.), but it's different from central Baltimore. Some parts of the west portal area of the Douglass/B&P Tunnel are like East Baltimore, though hillier, while others are what's left after you clear out for a highway, etc.
I couldn't have been happier with my Amtrak/MARC bike trip to Mt. Royal and UB, where I found good food before the train back. (Always pack a lunch if you have time before the train I say.) It just happened to be vegan lasagna, but it was amazing, as the kids put it. The bike charge on Amtrak and the folding luggage/bike rack is not ideal, but after searching all over for the required bungee cord for taking a bike on MARC, I found they really don't care, and even had an entire train car painted with bicycles.
