Of course it is better to have batteries in the same bank close together, as you already know. However, it can work OK with them separated as you suggest. Mine have been so for almost 15 years.
I have six golf-cart batteries totaling 675AH. Four are beneath the aft cabin
berth to port, while two others in the same bank are located under the nav seat on the starboard side, along with a separate starting battery
. All are flooded type.
My 1-2-ALL-OFF switch is wired in the conventional way, with the port-side batteries on position 1 and the starboard batteries on position 2. I LEAVE THIS SWITCH IN THE ALL
POSITION, effectively combining all six golf-cart batteries into one bank. There is a separate ON-OFF switch for the start battery.
The banks are connected with AWG 1/0 wire, which is none too large. The trick in making this work is to use large cable. AWG2/0 would be better for a run as long as you're contemplating.
The 20A battery charger is a bit small, but shouldn't have any trouble at all maintaining three or even four group 27 batteries at dockside. If you were actively cruising and drawing heavily on the house bank, you'd probably want a larger charger (50-75A) for faster and fuller charging
during overnite tie-ups.