Word is and forever is likely to be imperfect. It is not Wordperfect! 
I was a contributor to that thread and stand by the assertion that you can do one or the other but not both. You can use the chapter numbering for your appendix figures or you can have them at a higher level in the Navigation Pane.
Little to be done about the Navigation Pane. Shauna's method is still the best. It is designed for handling figure numbering and the Table of Contents.
I suppose you could use Heading 2 or 3 only in Appendices. It would tend to make the numbering a bit wonky.
How to create numbered headings or outline numbering in Ribbon Versions of Word by Shauna Kelly
You can put the beginning title Appendices in Heading 1 style to separate them out. That is:
In the Table of Contents you can easily correct formatting.