If you want the navigation bar to be fully transparent at all times, just remove the hex value in Customizer > Colors > Primary Navigation > Background.
I have used the customiser to set colour of primary navigation bar to a transparent colour. This is working for the sticky menu, however the primary menu before scrolling down the page isn’t transparent. I would like them both to look the same? http://gp.workingsheepdogtraining.com/blog/. Thanks