I'm not sure why wye vs delta matters here. Both are 3-phase transformer configurations that produce 208v between any two phases since, in either case, the phase are 120-degrees apart.
For reasons of efficiency, 3-phase power is used in most industrial and commercial settings. It also can deliver more consistent power since the ups and downs of the phases balance out. This is important for heavy motor loads, etc.
Single phase power is commonly used for residential use. Two single phase 120v supplies 180 degrees apart have a 240v difference. Thus is why homes get 240v.
Single phase power is usually used for terminal delivery to residential just for the simplicity and reduced expense of the wiring, breaker box, etc. Most residential loads, even motors, aren't three phase, unlike large industrial motors which, for reasons of efficiency, not wanting a big starting cap, etc, are 3 phase.
As an aside, as I understand it, residential single phase power is normally derived via transformers from a single phase from distribution 3-phase power by center tapping a transformer winding, giving two legs 180 degrees put of phase, so the 120v gets doubled to 240v.
I'd imagine that most marinas are 3 phase. That the common case for non-residential delivery in the US. And it makes sense for large pumps and big boats.
If mainship uses an isolation transformer that commonly divides across two 120v legs (120 degrees out of phase) to get 104v, it would be easy to call that a blunder, but that's not quite the whole story.
What's the alternative? Imagine configuring it for the common case for commercial marinas -- and then someone parks at a residential dock with singe phase service. Now the transformer is delivering 277v to systems designed, in some cases, for as little as 208v. That ain't good.
They'd need to pony up for the expense, complexity, and reduced reliability of an auto variable transformer. Or, they'd need to provide a switch to select among taps -- which a user could set wrong, putting things back into the unsafe 277v to 208v appliance situation.
This situation is common to more than mainships.
Most of the larger boats at my marina have step-up transformers to solve exactly this problem, especially with AC units. I attached a few quick photos.
I'd recommend adding one by your shore power pedestal. It's the common solution to a common problem.
I'd also recommend figuring out how 104v is becoming 90v or how 208v is becoming 180v. 13% loss is a lot. I suspect high resistence connections somewhere -- somewhere getting hot and that might get hotter, perhaps?