"If the houseboat is my residence, then it's a residence. "
Who said HOUSEboat? You said BOAT. While most folks might consider a houseboat to be a residence, most enforcement personnel consider a boat (other than a houseboat) to be a vehicle, and not a residence, regardless of who is living on it.
Ignoring that issue, what you have is the verbal and unproven opinion of some guy who picked up a phone. That is a very dangerous foundation tpo build upon. Get a written formal "advisory opinion" from a state law department or an AG's office, and then you have something you can take to court--or show to a watercop. Some guy on the phone? Come on, let's go pearl diving in the shark tank.
And, fwiw, if MD is like most other states you won't be allowed to discharge a firearm within 500 feet of a road OR residence, unless you are on private property in an area that specifically does not ban or regulate firearms discharges otherwise. So if your boat is a houseboat and a residence, and you discharge your shotgun from the deck? Catch-22, you might get a summons for discharging a firearm within 500 feet of the residence.
Some guy on the phone? Might just be setting you up. After all, Maryland IS rightfully proud and famous for being "the 55mph speed trap on I95".