You're thinking too much in exceptions.
The way I said it, is the way it is.
And yes, if mountains are poking over a see of clouds you'll have to use rts in the cloud node, not in the atmosphere.
And Porcupine is right about his example.
You should also be able to get rays without rts, but when more accurate calculation/shadows is necessary then rts comes in for rts in atmosphere.
Martin