So it turns out that I needed a more complex solution for nested prefabs. My game has a menu based upgrade system where the player must upgrade a building with facilities. I modelled each building facility with a GameObject Prefab. I have different stock buildings that have pre-arranged collections of facilities. Buildings are themselves game object prefabs.
I went with Prefab Evolution. it is pretty slick, although It seems to need to reindex (Check Prefab Dependencies) things every once in a while. I've read some comments that this could be slow for larger projects. So far I haven't noticed any big hiccups. For 25$ -- worth.
