I've also been looking for a way to do that, and found that you could save as subassembly both stock and KIS containers, KSP then will save their contents, and you can essentially copy containers with saved content. Of course, it doesn't work with mirror mode still, but you can place container mounts in mirror mode (not necessarily KIS one, it could be any part with free node, but mounts, docking ports, or nose cones works best for me), and place containers one by one as subassemblies.