I have a Mosaic Manufacturing Palette I use for multi-color prints. With the palette you use models setup for dual extrusion, center them on the build plate, and use multiple processes then set a different toolhead for each piece of the model. If you try to scale the pieces of the model they become uncentered and can not be auto aligned anymore. It appears the models are referenced on corner of the model when scaling and not the center which causes the shift.
Now if I go and create a printer profile that I can use the dual extrusion wizard with the models scale properly. The dual extrusion wizard is a pain to use as it doesn't handle more then two colors very well.
-Rob