You can change the color on the input window instead. Select the Adjust Plot Properties button (by default it is just to the right of the Find (binoculars) button. Once you adjust the color on the resulting dialog, which is docked along the right side of the window, press the Apply button.

Any new files that you create in the same folder will use your 3D Viewer Settings from Config. Configuration settings will not change the pipe color in an existing input file unless you then delete the .xml file, which can only be deleted if you are in piping input or output so that the ".c 2" file is expanded.