I'm sorry but, I can only repeat and confirm this can ONLY happen when there's another scenery in conflict OR by a wrong order in the Scenery Library, which wouldn't matter much if you don't have any potentially conflicting sceneries, but if you have, the order might be important, although it's always best ( either to fix potential conflict but ALSO for performance reasons ) to remove the potentially conflicting sceneries anyway, and not rely just on the layering order.
As I've said, we don't set *any* order in our installer and we don't try to change it either.
When NO 3rd party utility to manage the order is used ( meaning there are NO <Layer> Command in ANY of the add-on.xml files of any scenery, which is how we DEFAULT TO, since we don't use it ), a scenery gets on top automatically if it's the last thing you install.
Instead, if you DO use a 3rd party utility to manage the Scenery Library, the order will then become controlled by you and that utility so, if you used one, just be sure our sceneries are on Top of everything else.
But as I've said, it's not always guaranteed that "just" having the scenery on top of the Scenery Library will fix ANY possible conflict. Some conflicts *require* the offending scenery to be removed so, if you have the scenery on top, and you still have conflicting objects, then you DO have a conflicting scenery somewhere, no doubt about this.
The only thing I can guarantee is we haven't changed anything that would affect the loading order.