do you have an example of the same models stacked up on top of each other without the procbuilding? because it really looks like you've just got bad lightmap UVs or not enough lightmap resolution
The black bleeding through is an issue but the issue I'm trying to work on now is the giant difference in lighting between some of the pieces themselves. I circled a few examples to show which parts I am talking about. It seems really odd to me that I'll have a dark area and the BAM! super light block thrown in the middle.