I'm not an expert on rail junctions and such, but could the D/E-as-subway connector look something like this:
with Huntington-Newton/Needham trains using the Pearl St junction and Huntington-Fenway trains using the Washington St junction, and existing Fenway-Newton trains going straight through, with one station serving them all in the middle?
Need to avoid building 2 of everything such as that double-flanked junction. That's just too much disruption on a mission-critical block.
Here's a rough sketch, not-to-scale of what might work:
It's a superstation mixing and matching branches, so logic would dictate it be like Kenmore: 4 platform berths, diverging and merging traffic sorted before entering the platforms. So let's take that setup and stagger it a bit with offset platforms so it can all fit...a Kenmore stretched like taffy. Assume that the D and platform level remains in the existing cut and that the air rights overhang can be extended a little bit west to cover over the staggered platforms.
1. Huntington tunnel is dashed teal line. I picked an alignment that underpins the Riverway overpass, splits the parking lot at Brookline/Pearl, and doesn't knock over any townhouses. But assume that this could shift around umpteen different ways on further study.
2. Dashed blue and purple lines are flyover/flyunders for the bi-directional junction. Assume this is approximate configuration too, but you get the general idea. The merging/diverging tunnels pull up alongside the D tracks in a slip ramp-like setup. Assume that that D outbound-to-Huntington inbound track can be widened out a a much wider loop half-loop under the Kent/Station St. intersection and passing under the westerly platforms to avoid the other tunnels and keep this all at ground + shallow duck-under level without stacking tunnels (I should've done that on the drawing, but forgot).
3. The Forest Hills branch is all-streetcar. Basically a negotiable variation of retained D-to-E surface trackage. And an at-grade junction at the surface that simply turns right out to/from Pearl. At-grade is OK because this is the lightest-frequency configuration and grade separated territory stays grade separated.
4. Platform pair 1 is basically the current platforms, shifted maybe a few feet east. All westbound branches feeding in/out of the Huntington tunnel use this pair out of necessity.
5. Platform pair 2 is underneath the current garage air rights, other side of the slip-ramp junction. All Kenmore-Huntington circuit service uses this pair out of necessity, and the inner tracks are free for passing to/from Platform pair 1.
6. Any service patterns that don't have an outright routing dependency on which pair of platforms they have to use, such as thru-and-thru Kenmore<-->D, get divvied up between the two platform pairs in whatever load-balancing setup makes sense.
7. Because of the duck-unders, you can draw a straight-line surface walkway between platform pairs (dotted white lines). Sort of longish, but logical. And then I just added an inbound/outbound overpass that doubles as an exit out of the cut to the Kent/Station St. intersection and whatever's upstairs in the air rights. Full fare-controlled station.
Only thing I haven't figured out is dispatching this so there's no scenario where a train (esp. an inbound) at Platform pair 1 is going to hold up a train bound for Platform pair 2. Since the block narrows a bit here you aren't going to be able to put passing tracks like you have around the other set of platforms, meaning there's a little bit of at-grade traffic management to do here.
That's probably a caveat solved by choosing carefully what service patterns get assigned to which platform pair, and my head hurts trying to do that math so let's just call that a dispatching TBD. "Software", not "hardware" in terms of the build. Any which way you are never stopped behind a train on the Kenmore<-->Huntington circuit through the parallel downtown subways and your probable Urban Ring boomerang routing, and that's the important part and potentially heaviest service pattern. Forest Hills, Riverside, and/or Needham are just plain old branches. FH and Needham likely with lighter frequency and shorter trains than Riverside.
Any way you slice it the volumes are still lower at BV than Kenmore so some partial at-grade traffic management doesn't foul anything important. Remember, the Central Subway just got a heaping shitload more capacity with the Huntington downtown bypass and the equally likely Urban Ring downtown bypass. If 1 every X happenstance trains has to pause because of an unloading train on the platform in front of it, they now have the breathing room to recover that loss en route to downtown instead of compounding it.
It's not perfect, but it solves for the "build 2 of everything" conundrum and doesn't disrupt the footprint of the block too much with this bi-directional junction stacked on itself under the widest point of the that disposable air rights garage. And Forest Hills just uses the dirt-simplest turnout, likely recycled from previously-existing D-to-E surface tracks, for its much-shortened and much sped-up journey to the streets.