The Addon Manager doesn't have anything to do with this.
The new installation system it's not an "Addon Manager" thing, it's the officially suggested addon distribution system for Prepar3D, and it has been like that since P3D 3.4, we are just one the first addon developers that adopted it, but there are others too.
So, the real issue is, that all 3rd party utilities that needs to read the scenery database, cannot continue to rely "just" on the scenery.cfg, but must be updated to support this new system as soon as possible, because there are going to be more and more sceneries that will come out in the future that will switch to this new method.
The file that must be read now, in addition to the scenery.cfg, it's called scenery_add-ons.xml, and contains an updated list of all scenery areas added with the add-ons.xml method so, it's very easy to read.