I think if you had a nice set of smart materials--or even just basic materials--for each part of your terrain, you could paint some terrain fairly easily with the current setup. Substance Designer would probably be a good place to start for creating the materials, and then just set them up in Painter with masks. You would end up with one giant texture map, but you could paint in all the unique details you wanted. I've painted on a fairly large mesh with a similar setup, and thought it worked great.