I just thought I'd pop in (I'm the RCI creator) and mention that I'm interested to see if a solution can be found, because I don't have the technical knowledge to figure any of it out myself. I must admit I'm more comfortable with the visual stuff than coding and figuring out mod interactions.
If a method is discovered to avoid the annoying bug, and there's anything I can do to make it easier to implement, I'd love to contribute. Ideally, I'd upload a DLC modpack or some standalone thing that works better than the current implementation.
I will say that, from what I remember--I haven't played in a while but I'm getting back into it--when I used RCI, I literally copied files into the assets folder and overwrote what was in there. Obviously that's not a great solution, but it avoided the issue with civ colors returning to defaults. I'm not even sure if the most recent changes I made were ever uploaded in that form, so if that's something I need to do, I can.
I also want to thank you guys for enjoying my mod. I never expected it would be popular enough that people would want to integrate it into other things, and I regret that I'm not experienced enough to be much help.