The atmosphere effect seems to be behaving correctly, i.e. becomes transparent (newOpacity=0.0) a bit before the "central lighting" appears.
If I understood correctly, you scaled the planets way more than they are in the game. The shader uses the collisionRadius uniform (which should be the atmosphere's radius, because it is a sphere) in the calculations. If you didn't apply the right scaling to this entity as well, it might happen so that at higher distances the planet and atmosphere spheres have roughly (approximated) the same radius. What I'm trying to say is that if, e.g., the atmosphere_radius=planet_radius + extra, and not planet_radius * X%, then that "extra" could be your culprit.
Also your screen has an extra overlay (the yellow E:D like reticule) - do you get the same result without it present on the screen (say, if you look aft but you have it targeting something in front)?
I cannot say I've noticed this behavior in game, i.e. the planets "melt" nicely when small enough.
The Reticle is just a model effect vector().interpolated to about 50000 km from the player at any one time towards the target. It is working totally independant and will target anything. Even stations.
Tell it to render nothing ? as in being totally transparent thus behaving like expected.
https://www.opengl.org/sdk/docs/tutoria ... iscard.php
Well, I went ahead and tested it with this instead
newOpacity = 0.01;
All i then got was the atmosphere. The planet itself vanished, I then began thinking that maybe it is a sort of overflow as the distance is about that of an usigned 32 bit int.