After a lot more experimenting, and a whole lot of waiting for load times, I think I have a decent answer. You're definitely right about the fade stuff -- seeing a sunflare through the planet isn't ideal!
It's a combination of parallax being tuned for stock scale, and the person who did the JNSQ patches for Parallax not doing anything to help things. I was focused too much on JNSQ because I used to play at 2.5x Rescale, and it was pretty much just like stock fo Parallax. So I figured it had to be a JNSQ thing that was "wrong". But the way rescale works seems to automatically rescale the Parallax maps as well.
So anyways, here's my results for making things look better:
#1 is to rescale parallax textures larger, which I think looks better all around (not so crisp and bumpy, can't see the repeating tiles)
// rescale parallax
@Parallax:FINAL
{
@Body[Kerbin]
{
@Textures
{
@_SurfaceTextureScale = 2.5
@_displacement_scale = 0.39
@_displacement_offset = 0.09
}
}
}
#2 is to shift the PQS fade to a spot that matches when Parallax is less prominent. I have two options:
a: this is what I'm using
@Kopernicus:FINAL
{
@Body[Kerbin]
{
@ScaledVersion
{
%fadeStart = 70000
%fadeEnd = 80000
}
@PQS
{
%fadeStart = 77000
%fadeEnd = 88000
}
}
}
b: This looks better in orbit, but my GPU (6700XT) can't handle it. Clouds stay high-detail until you get out of PQS, and looking down at Kerbin from 125km was pushing me under 30fps. If you have a good GPU use this.
@Kopernicus:FINAL
{
@Body[Kerbin]
{
@ScaledVersion
{
%fadeStart = 100000
%fadeEnd = 110000
}
@PQS
{
%fadeStart = 110000
%fadeEnd = 130000
%deactivateAltitude = 135000
}
}
}
Both of these use :FINAL which is not good practice normally, if anyone else picks this up to incorporate into some mod patch.