You could 'cut the corner' on the common from Charles St. South to Tremont, and then build the wye along Tremont, just a little bit north of Avery St. Trains from the west then could enter Boylston St. Station from the north and then continue into the tremont st tunnel. Trains from the park street headed to the back bay could either bypass boylston on the wye and then under the common, or continue through it as they do today, depending on capacity etc.....(might be an opportunity to evict that non-standard curve from the system, for example)
So yes it's extra build, but potentially easier than a Stuart St subway
n.b. 'could', not necessarily 'should'... its an option...
The whole point of reusing the abandoned Tremont subway and building everything from scratch along the Pike is to avoid doing any construction in the historic core. If youre going to do what you suggest you might as well just go via essex.
I should have never mentioned Stuart Street, I was just trying to give a bit of historic context. A Stuart Street subway should not be built, and is not proposed by me or anyone else here. The Stuart Street routing has been superseded by Marginal Road along the Pike trench (which is a better routing anyway, since it gets you to Back Bay Station right beneath the garage).