CC's main entrance is literally staring at where the ex-Thompson Square stop's main entrance was about 1300 ft. up Austin St. The only transit loss in the middle of the neighborhood when the El went away was that the 92 didn't pick up at the main entrance any longer. They arguably got hit harder when their pair of Green Line branches on the 92 and 93 out of North Station got bustituted.
City Sq. did lose easy access, but there was virtually nothing left of City Sq. in the mid-70's to serve, and the Navy Yard was a pit of despair at the time it closed. If redevelopment out there is not getting adequate transit service that's a frequencies problem on the 93 to attack first and foremost.
All signs point to a shitty local bus route problem fixable by making frequencies less shitty, reshaping routes, or adding a peak-hour short-turn route to the Navy Yard and Spaulding. The only way a trolley line ever gets out here is if they start running heritage trolleys along the Greenway out of Haymarket/GC, in which case plunking some tracks on the bridge for a "Freedom Trail Branch" is not a too-far-fetched. But there's no upside whatsoever to the Green Line for sending a dense local-stop route out there. It runs in direct conflict to every other GL expansion goal that's all about fusing the system with the Urban Ring or linking light rail to the biggest bus transfer terminals.