That's... bizarre. From where I'm looking at it, it seems like the opposite is true.
Is there an actual track map somewhere?
Sort of:
http://www.dbperry.net/mbtacommuterrailnetwork.pdf. From 1993, very crude, and doesn't give a lot of detail of the Beacon Park area.
The loop is only used for turning CSX locos and for fueling. The Amtrak/MBCR equipment swaps reverse direction under the viaduct. Tight loops are a higher derailment risk (albeit at ultra-slow speed), especially when going through a dozen manual-throw yard switches to reach one. So it's simpler to just change ends on a siding. This is why using that loop for revenue service wouldn't be a swell idea even if the track got upgraded...if it can't be widened and if there's probability of a couple negligible derailments per year on the crawl around such a tight loop that's an equal number of probable PR hits per year where a train full of irate passengers have to board shuttle buses underneath the dank, noisy, smelly viaduct. Not worth the hassle.
It's way too narrow to shiv in a wye. By the time the GJ inclines down to grade it's roughly at the NW corner of the BU Fine Arts building and only separated from the Worcester Line by the literal width of the viaduct. The turning radius of a wye spanning 8 car lanes would be too narrow for a commuter rail coach and a bigger crawl-speed derailment risk than the loop. The geometry's not just tight...it's tighter than Amtrak's and the T's car design margin.
Does Worcester to North Station even really need the Grand Junction?
Why isn't Worcester-Fitchburg-North Station possible?
The Pan Am Worcester Branch goes to Ayer, not Fitchburg...so you have to take the west leg of the Ayer wye, go 10 miles out of the way to Fitchburg, and reverse. Worcester Branch is also incredibly twisty track because of the hills it weaves around, and currently unsignaled and 10 MPH its whole length because Pan Am can barely be arsed to maintain it. Any other route such as the Worcester Branch to Clinton, then Fitchburg Secondary fromn Clinton-Fitchburg (with restored track from downtown Leominster to Fitchburg) requires 2 reverses because the cemetery in Clinton makes that former junction NB-->EB / WB-->SB only. Yes, the T's got perpetual trackage rights on the Worcester Branch. No, they didn't acquire those rights because they intend to use it for anything other than equipment swaps. Its future utility is Worcester-hub commuter rail mid-century, not some godawful scenic route through small Worcester County towns that takes an extra 40 minutes of twists and turns to get to town. That will never ever ever be part of a Boston one-seat commuter rail route.
Grand Junction is the only logical one. No question at all. Just keep in mind that Cambridge's bitching about it is because the state started flapping its gums about service before even describing what basic grade crossing, vibration, and other mitigation it would entail on just the vanilla upgrade from Class 1 to Class 3 quality track. Tim Murray was merely being an insensitive clod the way he pitched it, and got what was coming to him resistance-wise. Put quadrant gates on Mass Ave. wired to the adjoining traffic signals and the queues will clear in 2 minutes flat. It's a low degree of difficulty problem to solve for the relatively light-volume 10-per-day frequencies they envision. Just because the GJ's crossings include Broadway, Main, and "MASS AVE." in bright lights doesn't mean they're particularly challenging ones to traffic engineer. I only think you need outright crossing elimination if it's DMU frequencies. So, shucks, if the Worcester Line gets "Fairmounted" it'll have to be the BBY/SS flank only with the GJ getting the lower frequency Worcesters and Regionals. I don't think anybody's going to find that an unacceptable compromise. World-class everywhere-to-everywhere service are what the N-S Link and Urban Ring Phase II are for.
For what it's worth there was a N-S spanning intercity train that lasted till the late-50's: the State of Maine, a joint NYNH&H and B&M train that ran NYC-Portland. Originally NEC to New London-->P&W main to Worcester-->Worcester Branch + Stony Brook Branch to Lowell-->Lowell Jct. and Western Route...then got re-routed New Haven-->Springfield-->Worcester-->Lowell. NNEPRA is already talking big things about "Downeaster Regional" runs out of NYC as an advocacy point. And the way they're pitching it is using the GJ to bootstrap a DE onto an Inland Regional after the Springfield Line is finished with its 110 MPH upgrade, the B&A goes full 80 MPH, and the slow-ass Haverhill-south portion of the DE gets full 80 MPH. Re-crew and change ends at North Station, but keep one timetable for 1-2 runs per day. Certainly a more immediately reachable goal than trying to re-create the old State of Maine route on crap freight track. It's multi-stakeholder stuff like this that the state should be waiting for before talking big game about Worcester to NS. The route's arguably just as valuable to Amtrak, and if some regional authority 2 states away is licking its chops at it too shouldn't we be waiting for the national players to be ready with their funding contributions first?