Mike,
I just caught up on some of the beginning questions here re: batteries.
I have the baitwell in the aft seat area so my engine batteries are right inside the cockpit doors and set outboard. The main 12V switch panel is Starboard, just amidship to that engine's battery and the Port hatch opens to one of the house batteries which is amidship to the outboard, Port engine battery. The second house battery is in the cabin in the back of the aft dinette cabinet, in a box.
I bought a set of those vinyl tubes with a bulb pump for filling the batteries. You just put the open end into a bottle of distilled water and quick connect the other end to the top of the battery cover (the original equipment plugs are replaced with plugs that connect to this bulb pump. Then, squeeze the bulb until it becomes firm and your battery cells are all full. I use these on my motorhome also.
You have to be careful not to connect the water fill tubes to batteries in different circuits. e.g., you need a separate filler set for each of the three 12V circuits, but it is OK to use one set on two batteries if they are in the same circuit. Safest is to use a separate battery filler tube set on each battery so you can evaluate the individual fluid levels as you fill.
Anyway, I think one could move the house batteries forward easily into several different areas if you needed more aft room. However, putting a hot, gassy, exhausty genset inside the hull is costly and risky. It'd be easier just to install a marine unit.
My dock neighbors are constantly having to clean debris out of their seawater coolant intake and I have no such problems using the Honda in a box.
John