I finally found out why object populations aren't showing when multiple surface layers are in effect in shaders. The objects sit on the main terrain, but each surface layer adds a small amount of displacement upwards. With enough surface layers, it will eventaully submerge your objects, and they will not show up.
What I had to do was change displacement multiplier to 0 and change the displacement direction to "lateralize normal" so if it adds it, it will only go sideways and not up. I tried just "0" and this still didn't work, so it required the "lateralize normal".
Anyway, what a pain it was to find this out. I spent days trying to find out why my populations weren't showing up, only to find out they were submerged by the multiple surface layers. It wasn't an object or population issue as I first suspected.