1) In the top menu (pictured below), what is the difference between "Printed Document" and "PDF Output"?
2) It seems that the TOC in the PDF output is built not from (not mirroring) the TOC in the HTML5 output, but rather, it's built from the files and their names in the Project Manager pod, and in the order in which they appear in that pod. Is that correct?
I'm not 100% sure but I think what it is doing is taking the default print layout and generating a PDF version of that. Personally I would always print from the print layout than run that option as you have more control.