You have a big confusion about this.
There's no such thing like a new or "master" scenery.cfg. We simply DO NOT use the scenery.cfg anymore...all sceneries are now added using the new add-on.xml method, which is the OFFICIAL and proper native method suggested in the SDK, we are just one of the first developers using it, but many will switch to it, and it's best if users start learning it, because it's going to be the new standard.
We explained so many times on the forum why this system is so much better so, best if you just search the forum, to find more detailed explanation.
However, the only issue with it, is that's not possible to rearrange areas added this way. Which, for airports, it's usually the best solution, since airports should always stay on top of everything. The system supports layering, just not from the sim UI.
I noticed that since installing GSX 2.0 a new Scenery.cfg became the "master" scenery file for the simulator
Not the case. This is just an internal copy of the scenery.cfg which is used by GSX ONLY, so it finds all sceneries, even those that has been added using the new method, together in the same list. The simulator doesn't know anything about it.