Oslo, which is a lot smaller than Boston although it has much higher transit ridership, suggests that reducing the number of trains that terminate downtown, and the number of station tracks needed to serve them, is possible, but also that it is unlikely that a multibranched CR network is unlikely to be set up so that all trains run through a single 2- or 4- track tunnel, at least if headways on the branches are increased to make the investment in eletrification worth it. Oslo looked a lot like Boston: eastside and westside networks connected only by a street-running line along the docks; Oslo had four routes out of the city, each of which had from two to four branches out in the suburbs. They did a massive tunnel project back in the 70s or 80s: subway on top and train underneath, with the train tunnel reaching off to the southwest from the point where the subway tunnel intersected an existing tunnel to the west (Nationaltheatret station on the T-bane and the NSB -- just now 2019 renamed Vy, but still the national pax rail carrier). They closed their West Station completely and replaced it with a four-track station (an eastbound cavern with two tracks and an island platform and a westbound cavern with two tracks and an island platform) next to and lower than a subway station at Nationaltheatret. Their East Station became their Central Station (Oslo Sentralstasjon). Heading east from Nationaltheatret, the four tunnel tracks split up into I think 10 underground, and become tracks 1-10 of an 18 track station at Oslo Sentralstasjon. Many trains run through, but many also terminate at Oslo S (all the long-distance trains (from Stockholm, Bergen, Stavanger, Trondheim, Halden/Gothenberg, and Gjøvik) and many of the suburban trains. If I had to guess I would say a bit more than half the trains that stop at Oslo S run through right now. That amounts to a train stopping at Nationaltheatret every minute or so in each direction at rush hour, every five minutes the rest of the day. The network is totally electrified. A few suburban branches have been closed to regular pax traffic or even removed, but new tracks and two multi-kilometer suburban express tunnels have been added. New business centers have grown up around stations in former small towns along three of the four routes out of Oslo, and Oslo itself has stayed vital.
In short, Oslo has a network of suburban trains that makes the T Commuter Rail look like a volunteer-run museum serving a skeleton network at inconvenient times. It is the kind of network that would justify the NS rail link, and it serves a smaller population than Greater Boston, with no city of the same size closer than Stockholm (6-7 hours on good lines, some up to 200 km/h). And even so, the tunnel project only eliminated one of the two terminals, and left Oslo S quite a bit bigger than South Station. So yes, the right rail system can lead to efficient, compact, urban growth with substantial ridership all day long, but no, it is not that likely that both N and S Stations could be converted into small underground stations.
What else does Oslo have? A single zone fare structure reaching twenty or thirty miles out, so that a ticket from a suburban station is automatically also good on the subway, bus, trolley, or boats within downtown Oslo, and vice versa: within the zones, NSB-Vy sells zone tickets the same as Ruter, the Oslo transit system, does, and you take whatever combination of modes you want. An Oslo zone 1 pass takes you all over the subway and trolley, on the boats and buses with Oslo, and on the trains within Oslo. There's no notion that a train should cost more because it's faster than the subway. It makes planning simple, and it lets the national rail system and the Oslo transit system serve different areas with different modes without making people worry about the fares (kind of like the wildest fantasies about an Indigo Line in Boston.