I don't think you can with Blender Internal, but if you bake with Cycles you can change the swizzle on normal maps. Baking in Cycles is kind of a wonky workflow for other reasons though.
@Chev did you use the proxy workflow in 2.79? If you find that it works better you, you could work on 2.79 anyway, and then use 2.8x for rendering (or whatever the reason you're using it now). 2.79 (the last nightly build for it) is my go-to at the moment. https://www.blender.org/download/previous-versions/
Ah, well if you duplicate an image node it still references the same image datablock, you need to click the little number first before editing the path - this will create a new image datablock. Its pretty much the same concept as with instanced objects.
@f1r3w4rr10r The "Split Edge" modifier does not create custom normals, it literally does split edges, that's why you don't want to export it applied. If you treat the model with the bevel shader as your high-poly, you don't need the modifier and it has the benefits that you can add geometry just for baking, which you…