I am not sure about your question, but I won't let that stop me (ha ha)
I use slmplify3d. I have a two head printer.
I make two models, identical, name them something like red sprocket and green sprocket, import them, superimpose them, make two setting files, ( the settings that the printer uses to print) Command one to print to a certain height, then call the next and have it print from the other heat to the next height. I could imagine identical superimposed files with filament changes to the idle head while the active head is working to print a vertical rainbow.
If you only need to alternate colors, no idle head filament changes needed, just a superimposed model for each Z height change, I think.
This only works if the colors are separated vertically by layers. I saw a tutorial on the Simplify3d site, I did not discover it, only copied it and it worked