>If I remember correctly isn’t most of the tunnel already dug because it was anticipated to be a priority project at some point?

Part of this section has a tunnel, but not it wasn't built in anticipation of this project. Rather, it was built in the 1910s when the proto-Blue-Line was a streetcar line. Tracks continued west from Bowdoin under Cambridge Street to an incline at Joy Street, where streetcars could continue on surface tracks to Charles Street and the Longfellow Bridge to Cambridge. There was even a Central Square (Cambridge) - Orient Heights streetcar line that used that tunnel!

In the 1920s, the Blue Line was converted to the heavy rail rapid transit line that we know today. With that conversion, the Blue Line became a more efficient, higher-capacity transit line, better suited to serving demand. This conversion also meant that the Blue Line's heavy rail rolling stock was no longer compatible with unpowered streetcar tracks, so the streetcar tracks over the Longfellow Bridge were removed, and revenue service through the Joy Street incline was discontinued.

For a few decades, non-revenue service Blue Line trains were towed through this incline to access a maintenance yard. The ramp portal was permanently covered in 1952. So, while part of the tunnel to the old ramp remains, that tunnel will need to be widened, modernized, and extended to accomodate this service. So much so, in fact, that it makes sense to treat this as a complete extension of the Blue Line tunnel from Bowdoin to Charles, rather than trying to force a square peg into the round hole of the 1910s streetcar tunnel.

I hope this explanation helps!