How do I protect my customized styles and templates?

Never give a drawing file containing your styles to anyone.

Therefore you should post process required digital deliverables the same way you plot plan sets.
Things end up on the right layers when you dumb down to DWF and ACAD.dwg, but no styles go along for the ride.

You can ruthlessly purge all unused styles if you must deliver in AutoCAD Civil 3D format.

The good set of Styles and Sets in our Framework for Civil 3D products can help you deliver a generic deliverables without your internal customizations.

The data is data in AutoCAD Civil 3D.

A well constructed project can be moved from your templates to "generics" really quickly with just a little skill and practice.