I don't think there is an easy solution here unfortunately. I would advise to split your object further so that you can use matching by name on this component too, but I suppose it's not always possible in your case.
If you want to go with baking two verisons and mixing them together, you can do that in Painter itself. You will need to bake your first version, export it and re-import it under another name, then bake the second version. You can then blend them in the layer stack (by changing the mixing mode in the Texture Set settings). For the AO you likely don't want to mix them with "multiply", otherwise dark areas will get double intensity. Just using the "normal" blending to go over specific areas will work better.
See:
- https://substance3d.adobe.com/documentation/draftpainter/latest/ambient-occlusion-painting-212304798.html
- https://substance3d.adobe.com/documentation/draftpainter/latest/normal-map-painting-212304814.html