Have you considered using Parasolid instead of C3D? It looks like it's fairly expensive and based on what the creator of Plasticity has said (he's also exploring Parasolid because of the same reasons that you have just mentioned), it could increase the price of Plasticity significantly. But apparently this third party library has even some support to move and scale edges, which is very interesting.

About the example of issues with face rotation, I found some issues when filleting after doing the rotation operation, but I did not save the file unfortunately. I will let you know if I can re-create it and will post an example.

Thank you.