Can I choose which appendices to generate instead of all twelve?

Yes, from version 1.9.6. In the wizard, after ticking "Generate appendices", a list of the twelve sections appears with a tickbox each and All / None shortcuts; only the ticked sections are written, so a book that needs just an introduction, a glossary and references costs exactly those requests. The same tickboxes appear in the book's workspace when you click Generate appendices or Regenerate appendices, preselected with the choice you made for that book. Sections you did not tick can be added later from the same dialog.