As discussed in many other threads, like this one:
http://www.fsdreamteam.com/forum/index.php/topic,16274.0.htmlIt's entirely normal that a scenery installed in the native P3D V4 way, will be greyed out in the Scenery Library, which is a way the sim is telling you that scenery is not loaded from the scenery.cfg, but from an add-on.xml package file, which is the suggested way to install sceneries in P3D V4 and, of course, it's nothing specific to FSDT, but it has been used by other developers, at least those that updated their installers to support the new system.
As explained in the other thread, the sim UI doesn't allow you to rearrange sceneries added this way (keep in mind that airports should always be on top), so you should either rely on installation order, and install all airports last, after any other scenery that can potentially conflict with them, such Global scenery areas, or use the free
Lorby Scenery Organizer utility, which let you rearrange areas added this way.