That's the way mine is wired now, but I have considered eliminating the combiner... The original reason for installing it was the same as you outlined in your post, but now I'm thinking: "Why not combine the forward battery with my house bank and make one big bank?

1) It's a lot of dead weight up front not doing any good 99.9% of the time(nl)2) It's never drawn down very far because the thruster and windlass are only used when the engine is running (unless I'm just letting out rode length).(nl)3) My house bank is never drawn down more than about 50% because I have a low-voltage disconnect set for 11.9v on my refrigerator feed.

I have a battery switch that lets me combine them any time, so it doesn't have to be a permanent change. The only issue is how the ground wires are wired to my battery monitor shunt.