I hate to mention this but, why messing with such a good simple installation and turn it into a complicated thing just like it is with P3D?
Installation doesn't have anything to do with this problem, and it doesn't bear any relationship whatsoever to the way we install sceneries in FSX/P3D, which used software modules to add features we don't have in MSFS.
You are probably mislead thinking the Addon Manager is used here ( it's NOT ) or has anything to do with this scenery ( it's NOT ) "just" because you see it's installed *there* but that's just a convenience which gives the following benefits:
- We don't place anything in the Community folder, JUST a symbolic link. This is obviously the cleanest approach, which gives you the flexibility to choose to install our stuff in a different drive/folder than the sim, which something lots of users wanted and appreciate. I'm not sure filling the simulator own folder with stuff is very smart and, of course, is not as if we are the only one using this method, since Orbx does exactly the same.
- Being inside the Addon Manager folder, is that we can use the FSDT Live Updater there and the clear obvious advantage of this, is that since the Live Updater is run at the end of the install, you'll get the scenery automatic updated to the latest version EVEN IF YOU DON'T HAVE THE LATEST INSTALLER, which in this case is even more useful to have BECAUSE we don't use the Addon Manager/Couatl in MSFS, so the scenery doesn't have a Trial, and so the installer is not always freely available to download at any time. But this way, at least, even with an old installer, you'll still get the latest updates. An obvious advantage of this, is that we ALREADY got an update yesterday, a few hours after release, which fixed the issue of some people floating over the terminal and *adds* animated people in the elevated glass walkways.
Of course, the problem you are having doesn't have ANYTHING to do with the scenery, or the fact it's installed in the Addon Manager folder ( again, it doesn't USE the Addon Manager!! ). As being found on our forum, the missing buildings are caused by ANOTHER SCENERY in conflict. For some users it was some freeware objects for Florida, in other cases it was a freeware scenery for Cape Canaveral, but it might also be something else we don't know about.
While with FSX/P3D, there's a Scenery Library with a way to set a priority, so we could at least say "place the airport on top of everything else", and this usually solves most of the conflicts, since our scenery obviously comes with proper Exclusion zones that are supposed to exclude all sceneries *below* itself, in MSFS there's no such thing, we don't know if Asobo/MS are planning to include some kind of Scenery Library page with the ability to rearrange things, but for the time being, you just have to be careful what you install.