Thanks Richard. I think an important step is modulating the cloud depth as well, and in this case I simply used the same cloud mask. It makes a big difference, even if not physically accurate.
I used a colour adjust node to reduce the white point of the mask as well. I adjusted nearly every parameter in the Cloud layer and Atmosphere nodes, spent hours doing so and eventually honed in on something that works. There was a bit of postwork done on all of the images including adding clarity and sharpness.
In my sunset renders I have a second atmosphere that is used to add more red colour (mainly to the water reflections) without affecting the main atmosphere too much.
