I actually thought about adding PSD as an option for export and placing different elements of a map into different layers there. That's what you are asking about more or less, right? I don't know though how complex this file format is - I wouldn't want to spent more time on implementing this than on the generator itself.
But is it that hard to remove the background and water areas from an svg? Each of them is contained within its own group which effectively should work as Photoshop layers (just a guess really).