Defer atmo/cloud has nothing to do with it I'm afraid.
Defer atmo/cloud means that TG will render it using the raytracer engine instead of the rasterizer engine (used for everything by default, except for objects).
God rays are essentially shadows in the atmosphere.
With that in mind then 2 entities can cast shadows into the atmosphere, terrain, clouds or both.
So if your terrain creates the shadows then indeed disable "receive shadows from surfaces" (default setting anyway).
If your clouds create the shadows then disabling "receive shadows from surfaces" won't help.
What you like to do then is to tell the renderer to render the clouds, but not the shadows generated by those clouds.
In TG your cloud node has a setting called "enable primary rays", this means that the renderer will render the clouds visible.
Below that you can find "enable secondary rays", which means that if a primary ray has "found" a cloud it will shoot rays from there which will calculate shadows, GI etc. of that particular part of the cloud.
It's probably not exactly how it works, but for me it kind of works to think of it like that.
So when we disable secondary rays in the clouds we should not have godrays anymore.
And that works.....howeeeeevvveerrrr...your clouds look totally different, because all the detail and shadows within the clouds themselves are also generated by secondary rays!