As Red Wing mentioned, the various subway tunnels were built at different times and for different purposes. The Green and Blue Line tunnels were both originally built for streetcars, while the Orange Line tunnel was built for elevated cars which were small enough that they could (and did in the case of the Tremont Street Subway) operate in the same tunnels designed for streetcars. Only the Red Line tunnels were originally built for large subway cars.
Later in the history of each, the various lines (with the exception of the Red Line, which always has operated cars of roughly the same dimensions as it started with) later acquired cars as large as the clearance envelope would fit. The Blue Line was converted from streetcar to rapid transit in 1924 but was constrained to operating cars about the same length as the semiconvertibles they replaced (~48 feet length), which themselves were huge in comparison to the 34 feet or so of the streetcars the line has started operating with. The streetcar fleet on the Green Line similarly grew through the semiconvertible age into the PCC era, and with the advent of the common use of articulation in streetcars broke the ~48 foot barrier into today's cars of 72-73' length, and soon to be even longer. The Orange Line had started out with wooden elevated cars about 46 feet length and eventually employed cars of 55 foot length (01100s) and later 65 feet (01200s and 1400s).
As an aside, the original tunnels within the Boston core were built by the Boston Transit Commission, not the BERy (or in the case of the Tremont Street Subway, the West End, Boston and Northern, or any of the other streetcar operators that eventually used them). Those earliest tunnels were and still are the ruling clearance restrictions on each line. BTC did have the foresight to build the Boylston Street Subway to Cambridge Tunnel (Red Line) clearances, and for the most part, subway tunnel construction under the auspices of BERy/MTA/MBTA after BTC ceased to exist in 1918, including the Huntington Avenue Subway, Kenmore Extension, etc., the Blue Line extension from Maverick Square to the east, and more modern day subway extensions, were all built with tunnels similar to Red Line dimensions.
The key to the discussion is that due to the enormous cost, engineering challenges, and vast disruption both below ground and above that such an undertaking would entail, there have been few if any real proposals or attempts to rebuild and expand the original core tunnels, notably the Washington Street Tunnel and the East Boston Tunnel, to larger clearances to allow for a unified fleet across all three rapid transit lines. For all practical purposes, the use of three separate fleets of cars on the rapid transit system in Boston is set in steel, concrete, stone, brick, and Boston Harbor mud.
Now, one could convert the Blue Line back to light rail and equip it with trains of Type 10s (and maybe connect it to the Green Line for the first time ever), and perhaps settle with using Orange Line sized cars on the Red Line, and thus arrive at one rapid transit fleet and one light rail fleet, but any and all of that would also come at an enormous cost and has perhaps more drawbacks as it has benefits.