I want to clarify one point on this for anyone who runs across this item in the future.
The code I posted went to all of the trouble to dissect vtkBooleanOperationPolyDataFilter (based on the paper cited) so that I could see (more or less) where the problem was occurring. As I found out, one can take the output from vtkBooleanOperationPolyDataFilter and run it through the vtkPolyDataNormals filter and solve the problem. I’m glad to see that worked.