I'm not exactly sure what the default Render Priority number is for photoreal, but the only way that may work is to find the appropriate landclass entry in the terrain.cfg and change it's RenderPriority value to one that is higher than that of the photoreal. Although, I really wouldn't recommend doing this if you will be releasing this scenery as it could screw up other scenery areas for the end user. Plus, honestly I have no idea if this method will even work.
[EDIT]
The safest way to go about this (If the priority method does work) would be to create and append your own landclass entries, however that takes a little work to do right. Someone else would have to walk you through this as I have only dabbled in it myself.
Those buildings/objects are visible in the sim because they are placed as scenery objects, thus they are not excluded. Autogen is typically placed with the Autogen Annotator in the SDK. This is how you would add trees and general houses on top of the photoreal.