Just to clarify, there is nothing wrong with giving your 2 extruders different retraction settings. For example, on the Extruders tab of your FFF settings, it's fine if you click on the "Right Extruder" on the left-hand list and it has different retraction settings than if you click on the "Right Extruder". So if you would have setup a profile this way and then clicked "Update Profile" to save it, that would be fine. You could then use the dual extrusion wizard and select that profile and it would be perfect.
The issue is that you created 2 processes with DIFFERENT settings for the these same extruders. Your "Color 1" process had the right extruder retraction distance set to 8.25mm and the left extruder set to 8.25mm as well. But your "Color 2" process had the right extruder retraction distance set to 4mm and the left also set to 4mm. So that definitely won't work if you try to use it for dual extrusion. Perhaps you intended to set the right extruder to 8.25mm in BOTH processes and then the left extruder to 4mm in both processes?
The S3D dual extrusion wizard actually automatically creates a process group to try to stop your from making these mistakes. Watch the 2 videos below if you don't know what that does.
https://www.youtube.com/watch?v=EbQfifnzL4Q
https://www.youtube.com/watch?v=qPufaJhyqME
So they've made it about as easy as possible to do things correctly. But of course, if you ungroup the processes and then start changing things yourself, it's definitely possible to end up with a configuration like the factory file you posted.