The 1909 report was followed up by an 1911 proposal and a
City of Boston Planning Board report from 1914 that spec'd out another possible alignment (and/or additional alignment) in addition to the "Wead Tunnel - so named as Leslie Wead produced the 1911 proposal" alignment carried over from the 1909 report. This alignment (see p. 14) would've coincided with the construction of "Boston Avenue", a proposed artery surface artery running from North Station down an extended Portland Ave through Haymarket, then proceeding through downtown between Tremont and Washington Sts to Kneeland St whereby the artery/tunnel would swing to the southwest and connect with the B&A main at the current Tremont St overpass by the Pike Ext.
It's important to remember that the 1880s-1920s constituted the brunt of the "Metropolitan"-era of infrastructure and public works in Boston (The Boston Transit Commission, MPC/MDC, Mass Highway Commission, etc were all birthed in this era) and were inspired particularly in later years by the City Beautiful movement that emphasized order, monumentality, large-scale public works and improvements to municipal services and infrastructure - something a new artery plunging through the warren of old Boston streets would accomplish. Copley Square and the western fringe of the Back Bay is perhaps the best remaining example of the goals of this movement, though South Station is certainly another good example (particularly the very orderly, monumental Beaux-Arts headhouse - the favored style of most City Beautiful adherents - and, at that time, the largest free-standing train shed in the world). However, these advocates were prodigious report writes, but never fully enacted their vision outside of virgin-land street networks like the Back Bay, a few widened boulevards (and Atlantic Avenue, a new thoroughfare), the parkway system, and parkland/landscape improvements. These tunnels are very much a part of this movement; they're interesting to look back on and think "if only", the 1909 report certainly elucidates frighteningly similar deficiencies the modern suburban transit system and draws the same conclusions drawn in nearly every subsequent report to date, but these are spec-plans and were never
really in serious consideration for more than a few years. Municipal improvement leagues produced some extravagant plans for Boston during this era, so it's par-for-the-course in that much of what was proposed never actually came to fruition.