Wow. Requested in 2019. There is a program (web based) that allows you to take a .STL file and paint it anyway you want. It will then split the model into as many separate .STLs for color printing. Many multicolor mixing printers out there now so this is not just the domain of the Diamond hotend. The program is SimplyColor3d. Your idea of Simplify3D doing the colorizing would be great but I think would be a whole new direction for the program. Of course I'd welcome it.
What we need from Simplify3d now is an easy way to setup "virtual" extruders for single nozzle printers. We (theoretically) would need unlimited virtual extruders for as many color combinations to be used so things like 50% extruder 1, 25% extruder 2 and 25% extruder 3 as "color 1" are possible. This would enable mixing of 3 primary colors at set percentages to produce more colors based on the mixing ratio. Like you said, scripts are cumbersome and limited. Also, I'd consider it a bonus if S3D could setup 5 primary extruders-1 nozzle as well since Diamond sells a hotend like that (true CMYBW)
Other "bonuses" I could think of:
"Rainbow" printing: go through all color combinations available by continuous color change.
Use of the model's inside space for infill and color change, to minimize the size of the "waste" block.
Use of supports for color change also to minimize the size of the color change waste block.