I'm not sure where the tunnel would've let out, but it was supposed to be a multi-phase expansion with the first leg just involving burying the Comm. Ave. tracks at least up to Packards with the portal onto the A, not the B. Maybe the portal was as far as Warren, but I thought at least the first phase of construction put it at Packard's. The B would've been abandoned from Packard's to Chestnut Hill Ave. (it's 1500 ft. or less away from the A up to Warren St. so only the residents up the hill would be S.O.L.), and the C would've taken over the BC terminus via Chestnut Hill Ave. and the remainder of the B trackage.
Phase II would've then extended the tunnel along the A (whether 100% underneath that ROW I don't know) and ultimately meet up with the Framingham line at some point and using that ROW for suburban service out to 128 and a park-and-ride station/CR transfer. The exact ROW was still speculative, and BERy didn't live to see it planned out. I'm sure there were many proposals floated in the 40's when they were dreaming up all those extensions.
This would've all been done in conjunction with an extension of the Huntington Ave. tunnel to Brookline Village, then taking over the then-still-CR Highland Branch ROW out to 128. And you'd also have some sort of conversion of the Tremont Lines, probably with a tunnel extension to the SW Corridor, and the Lechmere terminus fanning out (as is the current plan) along the Lowell and Fitchburg ROW's to 128. The remaining surface trolleys--Arborway, BC/Cleveland Circle, Sullivan via North Station, and the Tremont lines--would loop and transfer at Brookline Village, Kenmore, North Station Under, and TBD (present-day NE Medical Center?)...plus maybe some sort of "71" trolley transfer from the A/Framingham line extension that would take over any remaining remaining surface A trackage that the tunnel ROW didn't serve. And THEN you'd get heavy-rail cars on the Green Line once all the branches were moved onto protected ROW's.
Part of the reason for doing this, other than to scale-up the whole rapid-transit system for the fanning-out metro area population and the need for park-and-ride commutes in the dawning auto era, was to save the inner CR routes that were being jeopardized by the failing financial health of all the private railroads (because this was decades before MBCR). As those went belly-up one by one all kinds of commuter routes as we know were being abandoned. The city could ill-afford to lose any service inside 128, so the rapid-transit conversion had a protectionism angle to it for the inner-suburb and outer-neighborhood stops. CR trains on the new rapid-transit ROW's would transfer at the 128 stops for local service, and any locos running thru to N/S Stations past that point would run express and skip the local stops. That way if any railroads were lost to bankruptcy only the far suburban commuters would be inconvenienced, and they could just drive on the new highways being dreamt up to one of the 128 terminals instead.