Split Method
During the modeling and printing process, I discovered that putting the protector over the cable routing ports would eliminate the need for two additional ugly plugs. 

Working with the manufacturer, we molded in a weakness in the rubber that would split when installing a cable derailleur, or protect the hole if the bike came with a wireless derailleur. 

After success with the split method, I found some parts of the chainstay needed more coverage. I also added indicators as to where the cable ports are.