The short answer is yes. As for details, I can't help right now other than an outline.
Turn on the macro recorder in visio and place then change the color of a connector.
The code to change the color of the connector should be similar to the code in other posts in this thread which should be adaptable to your needs.
I did not distinguish connectors, so just placed the default connector between the shapes I had interest in.
If you ALWAYS have single connector leaving a shape then you can just a connector color to the shape row in the input worksheet.
If there is a chance for multiple connectors, you will have to add a separate entry for each connector and remove the default connector code that I used.
Very late to the party but i am having issues adding a Phase - I get the message "Separator cannot be inserted, A separator must be dropped on top of a cross functional flowchart". Anyone else come across this/ found a work around?