I have not seen these batteries used in the small boats that I see. Just my opinion, but the 25ft and under boats that I see are manufactured and sold to dealers without batteries. The inboard/outboards have alternators (like in a car) and the outboards have either the magneto that charging that the 20 HP Honda has or the larger motors have the car like alternators.
The dealers provide the batteries. In most of the cases that I have seen, most dealers want to minimize their cost and maximize their profits, so they put in a no name basic lead acid battery. If the customer has to change it in a couple of years, then the dealer has an opportunity to sell another battery.
From what I have read at other sites since you posted this, this LiFePo4 battery system is lighter, longer lasting, has better discharge characteristics, and recharges much faster. The drawbacks that I see are that it needs a battery management system to limit overcharge, overheating, and assure even cell charging....and it is more expensive.
Most everyday pleasure boaters do not seem to want to worry about this type of improved technology yet....they are familiar with the car like battery.
Just my opinion.
I am seeing more of this with electric boats and the torqueedo electric outboards. I am surprised that the serious fisherman have not gotten more into these with their trolling motors.' They make a lot a sense for someone that spends a lot of time or go long distances on the water
Back to the last suggestion about the diode in the charge line.....nice idea, but if you put it in the white charge line (the one with the 20 amp fuse in it),, it would probably do as suggested for charging.....however, current needs to flow both ways on that lead. That lead draws current from the battery to supply the voltage to the key switch (for starting and gauge power...then it feeds current to the battery when the motor is running and charging.
Unfortunately, the regulator/rectifier on the 20 HP is just a black box that works. Since we are dealing with a ton of unknowns about it, it might be worth a call the Honda Consumer Relations and see if they can hook you up with someone at Honda, that is more knowledgeable of the inputs and outputs of the unit. I doubt that they will give you design help, but maybe they can give you more information on its strengths or weaknesses if you just cut it off and on as you would like to do. Either you are going to get a "you wanna do what?" or may get some good info. It may be worth a call. Their number is 770-497-6400.
Mike