I'm also interested in this topic and how to improve the process of exporting building hierarchy. We store our 3D models in a CityGML database. This is the workflow I'm using, it's not optimal and there is quite a bit of work involved. But once it's set up it's quite fast.
Step 1:
Write the rule in a way so you can choose what is generated. Example create a attribute, say "Buildingparts" which controls the generation of all the building parts. "Building" generates the entire building, "WallSurface" generates walls... and so on.
Step 2:
Using python. Iterate through, and export each building part as a KMZ, as well as a csv text file containing all the attributes for each building.
Step 3:
Join the KMZ with the csv and export. We export as CityGML using Safe FME.
