You probably need a higher value for GI Sample Quality. 2 is usually not enough to get consistent results. All of your other settings look good.
The few times I have tried to merge different images, GI Sample Quality 4 was usually sufficient. I think I used 6 once, but you may need to user higher. Atmosphere samples can sometimes affect consistency across boundaries, but this is unlikely to be a problem with the high amount of GI Prepass Padding you have set. (In fact I have never needed more than 0.1 for padding, but this really depends on so many things like image resolution, detail, GI relative detail, blurring etc.)
Matt