When selecting multiple process for a single print job, S3D currently calls each one a "layer" (along with all of the legitimate layers) in the generated GCODE - this makes it less than "simple" to manage color changes, or any other task, which would potentially require a manual intervention. Differentiating between the two would allow for easier use of the {REPLACE} function in the Scripts section - allowing a user to use "{REPLACE "; process" "M600\n; process"}" rather than having to locate the precise "layer" which identifies the process and using "{REPLACE "; layer X" "M600\n; layer X"}" (as an example).
Alternately, adding GUI functionality (like a tick box) to call for a color change between processes might be a more graceful option.