Well, you can thank the years of corruption in licensing practices, such that the State controls licensing authority not the City of Boston (and capped the number of available licenses). And ABCC at the State level is not exactly corruption free in its history. It will take an act of the Legislature to change this, it is not under City control. (The City of Cambridge, on the other hand, did manage to get home rule on this topic, and has many more licenses per capita).
Also, there are Beer and Wine licenses that are available for less, which many mom and pops opt for (and do fine with).
JeffDowntown -- as usual with all things which seem absurd in Boston there is some history which must be appreciated
Point 1 -- Boston is one of the few State Capitals which is also the largest and most important city in the state
Point 2 -- the rivalry between the Olde Garde Yankees [Episcopalian] and the newcomer Irish [and later other European Ethnics] who are mostly Catholic.
Point 3 -- Prohibition and its repeal
So here's the scenario:
In Boston circa the Revolution and early Federal Period there was a tavern on essentially every block. This didn't change as the city grew slowly at first in the 19th C and then rapidly with the huge influx of the Irish.
As the Irish begin to take power [politically] in Boston circa 1900 as Democrats, the High and Mighty Yankees [Republican] -- aka the "Brahmins" start moving out from Beacon Hill and the Back Bay to places on the North Shore [e.g. Manchester by the Sea, Hamilton, Ipswich] and to the western suburbs [e.g. Wellesley, Dover, Weston] all connected by Commuter rail with their economic power base [i.e. State Street]. Yankee Republican political power is then vested in the largely suburban dominated State Legislature which of course sits in now Irish and Democrat Boston.
Republican Governors and a Republican Legislature enact laws to control the Democrat and Irish Boston, which the Yankees think is to unruly and Catholic. This leads to a surprising amount of Metropolitanization ie. the MDC which is a creature of the Governor and Legislature. It also leads to the Legislature and Governor having disproportionate amounts of authority to all things Boston such as the Alcohol Licensing and Taxi Licensing. It also establishes a permanent Tug-of- War between the State and the City.
Now Post WW II -- the Legislature changes from being a Republican Fiefdom to being Urban Democrat dominated -- Republican political power is limited to the Governor and other State-wide offices. One of the ironies of this is that the Irish finally in charge politically still feel oppressed by the Yankee bankers and industrialists -- as a result when ever the Democrats capture the Governorship the Legislature passes increasingly burdensome and onerous taxes and regulations on the business community. This has the effect of stifling Boston's growth economically during what for the State as whole is a boom period circa [Rt-128 "America's Technology Highway].
A lot of strange stuff comes from the above including the price of a liquor license or a taxi medallion. Another consequence is strange highly non-linear property valuation as the Irish Mayors try to put the tax burden on the Yankee bankers and industrialists. Another bizarre consequence is that as the alphabet soup of State Agencies are created to serve the Metropolitan area -- they are dominated by the State Legislature and Governor. Note that this happens despite the fact that the Legislature is now controlled by the same Irish Politicians who control Boston. Eventually the newer-commer Italians skip directly to the legislature and bypass Boston until Tommy Menino.
Finally, other ethnic groups who come-along later and blacks who have been in Boston since the Revolution are still waiting for their chance to follow the Irish and Italians to political power. Note that ironically, while economic power is still largely in the hands of the Brahmins, that some of the newest emigrees from Greece, Indian Subcontinent and China and Eastern-European Jewish Bostonians [concentrated in places such as Newton, Brookline, Lexington] have made a lot of economic hay and now stand near the top of the philanthropic lists [and get a lot of naming rights to things once the exclusive domain of the Brahmins].
While the above is not exhaustive [and may have some minor errors] and is not thoroughly documented -- it should give some of our newer members a sense of why some of these strange situations exist. Note that some of these may seem corrupt but are actually mostly the result of a century long power struggle between Boston and the State. Remembering that while Boston is the dominant economic engine -- politically it is just a line-item no different than Revere.
Postscript -- the GE story as it is unfolding is an interesting sidelight as the Irish [once again] Mayor is best buds with the Yankee [once again] Governor -- go figure.