My only last thought is that the 45% number for the desel engine seems a bit high, perhaps that number is a train engine or a power plant operating at optimum RPM? What's a small boat engine get when running at 1/2 or 2/3 throttle?
Train engines tend to be diesel-electric (i.e. Hybrid minus the batteries) and this would also have some benefit on a yacht - a bigger one at any rate.. There are a few ocean racing yachts still around from the 70's and 80's that used hydraulic drives for all the same reasons.
The figures are beyond me, but I'm not sure you're comparing apples with apples..:
1. A diesel engine in a boat gets throttled anywhere from idle to 100% with different fuel consumption at each throttle setting ("efficiency" if you like - at some throttle setting it will be "most efficient", but Murphy's Law states that max efficiency won't occur at cruising rpm..
2. A diesel generator in a marine Hybrid installation runs at "max efficiency" all the time i.e. the ECM selects the optimum diesel engine speed to match the load, which will be either (a) running the motor or (b) charging the batteries or (c) both.
This means that, in terms of "fuel efficiency"/"energy consumption"/whatever, the Hybrid will be far more fuel efficient under nearly all conditions than a straight diesel engine - offset by the cost of the batteries, etc, etc.
If you take a Hybrid car for a spin, you'll quickly see how it works..