There are a bunch of possible solutions for that, though. A lane of the Surface Road between Summer and Lincoln could be handed over to transit use. Bear in mind, this will get the full SL4 + SL5 frequencies, currently planned at 4 minute headways at peak. That's a pretty strong argument for reclaiming some of the public ROW.
Alternatively, a contraflow lane could be added on Lincoln, with buses heading south to pick up the current loop alignment via Essex Street.
Or, given that Summer Street will also be playing host to the high frequency (T)7, we can hope there might be bus lanes and other infrastructure going
through Dewey Square, which could allow Silver Line buses to loop around the Federal Reserve Bank Tower (providing better transfers to the Red Line, the commuter rail, and better access to the Seaport).
Or, on that note -- and hear me out on this --, the new SL5 could do a +1 extension to Courthouse:
View attachment 59420
Seaport jobs are still concentrated more toward the western end, so while this extension would not eliminate all SL5 <> SL1/2/3/W transfers, it would absorb some. Plus, it would actually make good on the promise of a South End <> Seaport connection. Importantly, traversing the Fort Point Channel via bus eliminates one of the more unpleasant elements of walking to the Seaport -- walking across those bridges when the wind chill is frickin' 20 degrees.