The Following is an opinion written by a gentleman who is an active contributor to the ABYC electrical standards.
Amongst the "experts" that comprise the ABYC Electrical PTC, there is significant discussion and debate on this topic. The question being, "why would you INTENTIONALLY cut the ground line between the boat and the shore power pedestal?" That is, after all, what an isolation transformer does.
The answer purports to be, "it opens the path for fault current to return to shore, so eliminates current flowing in the water." Well, it also eliminates the fault clearing path that trips shore power circuit breakers, and it's what happens in fault conditions that codes are intended to address. And the transformer, and the wiring of and around the transformer, can still fail in a way that puts current into the water (the very thing they are supposed to prevent). So in that overall conversation, I'm persuaded that the polarization wiring configuration is a better option than the isolation wiring configuration, if you're gonna have a transformer aboard at all.
Transformers 1) are heavy, 2) need a lot of surrounding open air space (because they) 3) throw off significant amounts of heat, 4) take up a lot of space, 5) are expensive, and 6) can require manual intervention which can damage boat electrical systems in cases of operator error. What could possible go wrong there? The most frequent sales point behind transformers is to eliminate galvanic currents, but there are also Galvanic Isolators to do that. In fact, with the polarization configuration, you are still gonna need a Galvanic Isolator. So "if money is no object," then why not?
Are there any suitable alternatives to transformers? Cheap alternatives, at that? Well yes, as it happens, there are. How about ELCI Technology? ELCIs are ground fault sensors that can detect in an instant (well, 100mS) if there is current leaking out of the electrical system where it's supposed to live and stay. They cost 1/5th or less, installed, what a transformer does, and they work just as well for fault detection. ELCIs (well, called "RCDs" in the rest of the world) weren't common in North America in 2005, but they became "required" by ABYC in 2012 on newly built boats. They are heavily recommended to be retrofit to existing boats these days (but I do acknowledge, they are no where near as "glitzy" as lithium batteries). And, the RCD technology Is also required on docks by the NEC, since 2011, so these devices are going to be part of our futures whether we like it or not, obsoleting shore power transformer technologies on boats.
So, galvanic isolator for galvanic currents and ground fault sensors for current leakage scenarios, is there still a role for isolation transformers?
Not too much in North America. The one legitimate need for transformers is in the case where the shore power provided by the utility is "dirty;" that is, waveform is corrupted past certain tolerance limits for a sine wave because of the distortion caused by power company customer loads in the neighborhood of your marina. This happens primarily in city and industrialized suburban environments, and sometimes in highly rural environments, so if you live in, and keep a boat in, an affected location, a transformer is still the right solution, because it smoothes out noise and distortion from the power incoming on utility company power lines.
Otherwise... And, unless "money is not object..." I recommend you invest in Galvanic Isolators and Ground Fault Sensors on the incoming shore power. The truth is, isolation transformers hide symptoms but DO NOT "fix" anything.