One think I've noticed is that the sun sometimes shows through the landscape as shown on the image. Sun altitude is 1 Deg
This is a known bug and will be resolved in future versions. For now you can fix it by turning on Raytrace Shadows in the Atmosphere Quality tab, however it will increase render time by a significant amount.
On the other hand I can make sure I keep the sun over my left shoulder :)
(Old photographer joke)
Lets just call it transparency feature until it's fixed.
Does it help if you turn off the 'visible disc' option in the sunlight shader?
Not that I remember it doesn't - not a showstopper by any means though
No, turning off "visible disc" doesn't turn off the sun glow, which is what tends to show though. Turning off the glow might fix it, but then your sky probably wouldn't look right.