voltage drop across the fail safe diodes affecting charge rate?
yes, you will need to either remote sense or turn up the controller to offset the FSD voltage drop
after seeing the breaker box, not sure i would want to get involved with this project at all.
the alternator power cable should go directly to either the battery or the switchgear that directs to either of two banks
but not any great distance in my opinion, and not through some cumbersome box with other circuits, again in my opinion.
going some distance is going to have as much or more voltage drop than a FSD at higher amperage.
looks like you might wanna think about getting an expert to take a look at what you have, draw up a schematic for you
and access what the hell you have there,, looks like frankenboat to me.

point being, i sure would not want to go to sea with a system such as that without a good schematic and a better understanding of the system.
as for the second alternator, that makes perfect sense to me, redundancy seems prudent for something very remote like being out at sea or on the moon,, which being out at sea is about as close to as one can get as far as being remote and not able to run down to the corner parts store.
if you decide to go the 2nd alternator, maybe connect it to go direct to the batteries and work only at specific times? such as in a failure at sea? or maybe its time to just upgrade the original to something much larger as steve suggests,, there is a time to make upgrades
and this might be one of them, just save all the oem stuff for putting back to original if you like later. i am all for keeping things stock, but
when it comes to safety, you gotta draw the line somewhere?
good luck
bob g