I don't know much about all the products you mentioned and what type of files they change.
And, there's no "rule" about how we do lights in a scenery. First, because not all of them are made by the same designer and, because each scenery is different: some uses default lights, some uses a combination of default lights and custom lights, some use custom effect with default textures, some uses default effects with custom textures, some use custom lights and textures even for runways and approach lights so, each one can be affected (or not) differently by any of the 3rd party products you asked about.