With respect to municipal taxation; many cities have a hotel/motel tax, the same approach would not be complicated, it's just that it's been overlooked I'm sure. They probably don't enforce personal property taxes as liveabords could be gone overnight, the marina owner would then be in a position to police residency requirements.
I would think that marina owners would rather have a certain amout of leased slips to ensure a breakeven position on a monthly basis. I know in my area the lake marinas get pretty lean in the off season and many simply close.
I have no idea what it might be like in a large city, say Boston, or what the liveaboard population might be, but I've heard living aboard referred to as a well kept secret. I'm sure the homless population has increased and any boat would be better than a box!
A boat is thought of as a luxury item, that notion could be revisted through marketing of better solutions, boats designed to be more of a floating home as the one selected. If designers could consider a modual system, say with RV materials I would think the price would be more affordable, especially for homebuilders.
Your comments on those future power alternatives are waaaay over my head, I'm a business guy not an engineering type...
I'd hate to see more regulation on inland waterways, but it may be in our future.