I'm not entirely sure I understand your question or concern, but in general, with a dual body regulator you have control of two different pressure lines. There are a variety of things you can do with two separately controlled lines. As I think you are stating, you can use one gauge set for your serving pressure, and the other as your carb pressure, or have two different serving pressures, or one for serving and one for low-pressure transfers, or basically any combination you want. And if you want to add manifolds to the mix, you can have several kegs at serving pressure, and use the other line for carbing multiple kegs, transferring, etc. Also, keep in mind, with manifolds you can serve multiple kegs off of a single body regulator. And if you get the manifold with individual shut-off valves for each port, you can get creative on serving and carbing off of a single body regulator.
Please excuse me if I have missed your question and simply restated what you already said.