Unfortunately (for automation's sake), there doesn't seem to be any obvious way to specify a single default output file. So you need to manually save whichever file you merged in to, and then refuse at the prompt to save the rest.
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.
