Hello! Thanks for the report.
I've been able to recreate the issue myself, and will work on adding compatibility soon.
That said, it is possible to get them to work together with the current version (0.5.4), it just takes a few extra steps - those being:
- Load the game without K2SO, but with configurable-nukes
- When the game loads, go to "Settings" -> "Mod Settings" -> "Runtime"
- From there, manually remove the "rocket-fuel=...," portion from each of the ballistic rocket part recipes (basic, intermediate, advanced, beyond, and beyond alternative)
- Add back K2SO
From the above steps, I was able to get the two mods to load together and start a new save. Only issue I noticed though, and plan to rectify with proper compatibility, is that the rocket-fuel requirement was no longer correct for the additional ballistic rocket-part recipes (not surprising given the above changes).
Hope that helps - do let me know if you encounter any other issues.