Eh, I figured as much. If I make my import preprocess plugin return a zipped folder, then it becomes impossible for me to add the original PDB file to my library. For now, I think my workflow is my best option. It creates my specialized HTML folder when I add the PDB file, then I add the HTML file to the Library.
However, I DO think I should make some use of the "calibre-debug" command and see if I can improve the Metadata import of a PDB file. That would at least save me a couple clicks.