You could just use Diffuse's center panel as the one to merge in to and save.
But there's no way to make it the one that's saved by default. You have to select it as the one to save, and then you have to refuse in the dialog that asks whether you want to save the other two.
Comments
So that isn't quite the same as Meld's left-, right- and center panels where the center is whatever output you want saved.
You could just use Diffuse's center panel as the one to merge in to and save.
But there's no way to make it the one that's saved by default. You have to select it as the one to save, and then you have to refuse in the dialog that asks whether you want to save the other two.