Maybe the flickering is caused by something else such as GI? I wouldn't dismiss the two-planet method yet. If you can send us a few frames (either here or the support address) we can probably narrow down what's causing it and suggest ways to fix it. If it really is caused by the proximity of the two surfaces, the Animation Check button might help.
Regarding the original Merge Shader issue, I've been working on some improvements which I hope we can release soon, but I wasn't able to really make it work well with the version you have, I'm sorry to say. A different setup might work though.