When I started learning about godarays I also assumed that the sun had to be above or indside the cloud layer,but upon further experimentation I find it does not.As show in the following images.i am not entirely sure what else it could be based on, I am thinking maybe arial perspective???Or how it is casting godrays at all in fact,but I have several in an upcoming collection with the sun set far below the cloud layer and all casting pretty strong rays..baffling to me honestly.

"Many are willing to suffer for their art. Few are willing to learn to draw."