For those in similar situations:

• not all rmv branches are created equally. For example, if you are a person of color, the Watertown RMV is a better choice than the one in Boston proper. It sucks and it shouldn't be this way, but that's the truth of the matter.
• if you have a system glitch that or a catch 22 like the OP, contact an Ombudsman. System glitches are common and difficult to override, and because of the power dynamics there is little incentive for RMV staff to bother fixing oddities. Sometimes even mentioning you are working with an Ombudsman is enough for your issue to be resolved, even if it was ongoing for years.
• If you registered to vote using the RMV be sure to keep an eye on your records to make sure nothing odd happened, least you lose your ability to vote. This can be done easily online and is easily resolved, but don't assume everything is fine
• If your understanding of the law is different than the RMV staff, be respectful and positive but clearly state what is going on. If you are friendly enough they will verify your understanding with their peers and admit mistake. If this doesn't happen it is often easier to try again at another date and hope you get a more educated teller.