Hello Fangschuss
What do you exactly mean by a "RUb only version"?
If you want the Atmosphere mod added to RUb, it's just to enable it over RUb.
What happens is, that you'll loose RUb murky water and RUb Env/sky colours.
If you want these features but also 16 km vis mod, then use RUb Env/sky files, extract .TGA's from RUb Env/sky files and pack them into Atmosphere mod Env/sky files.
Take scene.dat from Atmosphere mod and set murkiness "4" with SH 3 commander.
Then you are close enough with RUb colours/murkiness and the rest from Atmosphere mod.