I am a little confused. You have a 2 input 3 output diode isolator which feeds two battery banks. If you were to connect the two alternators directly to the batteries you would lose isolation. If you ran the house bank down at anchor, you would also run the starting battery down and then couldn't start the engine.
That is why you have isolators, but as you note they also have a significant voltage drop. A combiner or ACR will solve this problem. But you also say you have an automatic relay and transfer switch. What does this do? You could probably use this one ACR to handle all of your battery combination and isolation needs.
It sounds like you have an electrical system that was cobbled together with no overall plan. I would find a good marine electrician to come up with a comprehensive plan to deal with your electrical system.
David
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