Does using Fair Go PDF raise issues under the Privacy Act or NZ Privacy Act 2020?

The tools don't create the risk that upload-based tools can. Cross-border disclosure rules (APP 8 in Australia, IPP 12 in New Zealand) are about personal information being sent overseas, and a tool that runs entirely on your device sends nothing anywhere. Your wider obligations for collecting, storing, securing and retaining that information still apply. This is general information, not legal advice. For the longer version, read what the privacy laws say about uploading documents.