tl;dr Kopernicus in CKAN RP-1 build works for me??
Just FYI... I've been fiddling with this ever since first posting... today I did another clean install of KSP 1.3.1 (in another new sandboxie sandbox), started a new game then exited KSP. Using CKAN I checked RP-1 and installed only what was necessary. Fired up KSP and it worked! No Kopernicus error!!
The only thing I can think is that my previous clean 1.3.1 installs were being corrupted somehow before I even tried RO/RP/RSS - I can't figure out how though because I'm usually very careful about such things?
I did see in the logs that when it wasn't working I was getting the shaderloader error that you reported on discord - so maybe you have a similar problem?
Anyways, if there is anything (files, versions, screen shots, logs whatever) I can do to help you spot differences just let me know.
All I have to do now is figure out RP-1 :p