Actual land elevation plays in your favor for this deep bore. Tremont and Washington Streets are the high points in elevation; the land falls off toward Arlington/Charles and South Station. The elevation change is around 50 feet, meaning the route deep under Boylston and Chinatown stations is actually a relatively straight shot from Arlington to South Station.Couldn't a green Line tunnel along Essex Street be deep enough to avoid undue impacts on Boylston Station and the Orange Line tunnel? If you started the tunnel to come off the existing Green Line tunnel between Charles Street and Arlington Street, begin dropping immediately and pass under both levels of tracks at Boylston Station (some underpinning of Boylston Station required ) and keep dropping (with a deep bore) to be well under any utilities and foundations along Essex Street, pass under the SB Central Artery tunnel, then rise up to meet the busway tunnel at SS, it seems that it should be doable.
The Post Office Square extension proposed and designed pre WW-1 had a similar trajectory on its west half: