Yes, you are totally correct about the editable text in NWP. And this is still the behaviour in version 3. My statement above about version 3 and drag-and-drop is wrong. I probably allowed myself to be misled by the layout in my test document.
Nevertheless: Yes, I would assume that since printing to PDF (i.e. saving as PDF from the print dialogue) from any of the tested programs (Nisus, Word, Mellel, TextEdit) uses the OS, it is the OS that renames the embedded fonts, not Affinity Designer. So the OS, then, not NWP in itself. I have also tried PDFwriter for Mac, though, and in NWP I have tried “Export as PDF”, and they both give the same result as saving as PDF from the Mac’s print dialogue.
Therefore, perhaps the question may be why the fonts are merged and renamed to something cryptic, and are reported as “missing”, only when the original PDF comes from Affinity Designer (still, only when the fonts are embedded as subsets), and not when the orginal PDF comes from Illustrator, from an Illustrator EPS converted to PDF by Preview or, as I just tested, from OmniGraffle’s PDF export, or from OmniGraffle with a paste into Preview.