Can't Change Shape Color

If you break out the AE project from the MOGRT file and open it in AE, you'll see that the colours of the lower third segment are all controlled by expressions linked to a control Null layer called "Box Width".  To change the colour of any shape layer, you need to change the Colour Control parameter on this null layer, not in the shape layer.  Or alternately you can disable the expression that links the parameter to the control null.

There are a bunch of ways to edit the color of a shape layer in a MOGRT file but since we have no workflow details or screenshots showing us the modified properties of the layer I have no idea where suggest you make changes. Give us some details and maybe we can help. 

You could also check out some of the Adobe tutorial on creating MOGRTs. Don't rely on YouTube, check the Adobe User Guide.