It appears that there may be several laws in play here, but perhaps the interpretation of those laws by the Massachusetts Alcoholic Beverages Control Commission, the brewers, and the Mass Brewers Guild that determine how growler fills work in practice.
The first law in question is the regulation on labeling. Nothing in there appears to prevent brewers from filling any growler, but the standard interpretation from both the ABCC and the brewers is that they believe it makes it illegal for them to fill any growlers other than their own, and that is the policy by which they seem to all operate.
As for retail establishments, there do seem to be some non-brewery bars that offer growlers, (see Ducali Pizzeria and Bar on this list) but those may be for on-premise use. There was a proposal for a bill to allow on-premise / off-premise licensees to do growler fills but as far as I can tell, it died in committee, primarily due to strong opposition from craft brewers who were worried it would cut into their bottle profits.
Beyond issues of distribution, the joint legislative committee also heard from industry members interested in allowing both on- and off-premise retailers to fill beer containers up to 64 ounces for take-away and off-site consumption. The bill, sponsored by Representative William Pignatelli, has caused some division in the industry between retailers and small brewers. “We think it would be a disaster for our business by cannibalizing our bottle sales, our only real income source,” says one small Massachusetts brewer. “We for one couldn't thrive in a situation where the profit on bottled beer transfers from brewery to store or bar.”