I believe the clearance issues restricting use of the modern high-cube refrigerated cars are likely under I-93 in the FX interlocking area and quite possibly on the NEP lead as well. But, it's been a while since I've been down there so I'm sure someone qualified on the physical characteristics of that area would be able to provide better information. Besides the clearance issue, there is a 263k weight restriction into NEP as well.
My mentioning of trailers and containers was of the intermodal variety once moving via Beacon Park, now via Worcester. What's left in the old lower-capacity reefers directly serving NEP are potatoes, the highest-density (lbs/cu ft) of the perishable commodities with lighter-density lettuce, celery, oranges, apples, pears, cherries, carrots and onions having migrated to truck, intermodal and higher-capacity railcars over the past ~40 years. (As a side note of interest and highlighting their age, some of those old reefers are of BAR potatoe-service origin, if they haven't already been retired)