There´s an issue with terrain elevation in all areas surrounding the civil airport indeed, not only in the FAMET one. I already detected that during edition. With default civil airport (no GCXO addons nor other addons for the area) the original FAMET area does what you describe, even if you place just one object in editor like a truck for instance. That happens while not using my FAMET addon yet so just when you edit anything in the vanilla game area.
Trying to solve it I added an exclussion rectangle to delete everything existing in that small FAMET area without changing the civil airport at all and I also included a custom terrain elevation with priority 10. That solved this bizarre issue it in my case at least and there´s nothing else I can do to improve it. Increasing my elevation priority to 100 for instance made no difference. Indeed when loading the addon source files in editor it goes below civil airport runway level for just 1 second but later on it follows my custom terrain elevation properly. However the addon works well in my case when it´s loaded normally in a regular game launch.
To be honest I have no idea about the reason for this issue. It´s the only addon where I have faced that… If anyone else knows the possible reason please comment it. Anyway, if you have Iberia WU and my addon already installed, you can try to rebuild scenery indexes by deleting all contents inside:
\AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache\SceneryIndexes
Game will create new indexes for all addons during game launch, so it won´t break anything but it may take a while. This may fix the issue in your case because that fix solved many other issues in the past with other addons that were not behaving correctly.
Cheers