As a Boston native and former GOAL employee (intern), I may be able to help answer some of these questions.
First, Boston is a GREAT city. Other than its gun laws (more a function of state law) and high cost of living, it is awesome. If MA was better about guns, I'd live there in a heartbeat.
You've already read the ban, I see, so I won't elaborate too much. It appears to me to be like the CA ban in that it names specific guns, and does not list criteria in the way that the federal ban does. So, the way I read it, if it doesn't say "AR-15" or "AK"-something on it, it's OK. That catchall provision at the end seems to be aimed at shorter barrels, stocks, etc., rather than clones. The "substantially identical" is probably void due to its vagueness - it's not specific enough, although I wouldn't want to be the test case.
Also, I have never heard of anyone getting nailed under this law, even people who were doing "something else bad". I doubt if many BPD officers even know about it, much less care. If the BPD firearms licensing people don't know or care, that should answer your question. Just don't go marching down Newbury Street with an AR-15 and I think you'll be fine.