This is one of the things that I find problematic in X-Plane -- the constant development brings both very good things, but also problems when stuff has changed and does not work anymore like expected.
Here are my observations and what I did about it:
1. The newly introduced default airports in 10.25 are ALL (hundreds of them) in one folder, Global Airports. First thing to prevent conflicts with custom scenery is to give this global airports folder the lowest priority among all airports (BUT a higher priority than meshes, if installed). You can do this by moving the Global Airports entry in the .ini file down, after your last custom airport.
2. Far too many custom airports do not yet have the proper exclusion zones. Ben Supnik says that such sceneries have bugs, but some authors see it not this way. As the exclusion system is a bit cumbersome (only rectangular exclusion zones are possible), many developers simply did not want to add exclusion zones at a time where no problems were visible. Instead some are hoping that Laminar reconsiders the whole Global Airports concept or makes airport boundaries work as default exclusion zone. Currently, what you can do, is to open the airport with OverlayEditor or WED and add your own exclusion zones. You will need exclusions for facades and for objects.
And here's a future problem that already comes upon us with the HD mesh:
3. In the future (with the scenery-recut, and already today with the HD mesh), many airports will have roads crossing the aprons and taxiways, because Ben Supnik and Andras Fabian decided that this way scenery developers have more flexibility. If the developer of a scenery does not create an update, the users can get rid of unwanted roads by adding exclusion zones of the type "roads, railroads, powerlines".
4. Also already visible in the HD mesh are airports where lots of trees are growing on the apron. Here the scenery developers have forgotten (or: Did not see the need for) exclusion zones for "forests". Again, users can add their own exclusions here.
To summarize: Since XP 10.25, and even more when the scenery recut is released, all scenery developers need to check their sceneries for the proper exclusion zones for objects, facades, roads and forests. Given the very high number of available scenery, this is a tremendous task ...