Specifically with InternalClassifierType and InternalNewExpression.
From examining the code it seems that anything used in the fqClassName makes it in to the import statement so I'm getting nested classes reference up in the imports rather than the class name.
Obviously w/o access to the referenced nodes the code can't figure out which '.'s mean internal classifier type, so maybe there needs to be a special character that resolves to a '.', but is interpreted as separating class from internal class, or better yet two fields fqClassName, internalClass or something?
As a workaround I'm going to generate static methods on the root class to construct the nested classes in question, and I can get by with using the superclass type of the nested classes to avoid InternalClassifierType. Maybe I should file a feature request if I'm not missing something?