Wow, that is quite the analysis.

Thanks for getting back to us about it!
About Kindle multi-level ToC, if you hit the top-level text, you go to that entry in the book, but if you hit the arrow on the left, it will expand instead. When you are in a particular section, naturally it will start out expanded so you can see where you are -- I get the feeling this was how you ended up doing it? It might not be the easiest to hit it, though it doesn't really give me a lot of trouble.
And I think I mentioned before, the ability to jailbreak and install a Kindlet that lets you add books over WiFi/SSH? The USBNetwork hack, that is, which comes from the same thread as the jailbreak itself, here:
https://www.mobileread.com/forums/sho...d.php?t=186645
EDIT: And about Sony Page Numbers vs. Kindle locations...
Unless the book has a Page-map.xml inside, those pagenumbers are auto-generated by the ADE engine, and correspond to 1 page=1024 characters of text. Kindle uses locations in much the same way, except that IIRC they are based on formatting as well, somehow. If a Kindle book is bought/checked out through Amazon's servers, it will likely include a sidecar "{boook-title}.sdr/{book-title}.apnx" file which contains pagenumber offsets that correspond to the actual page numbers (with actual accuracy/validity). I prefer the locations system since they don't lie to you about what they are, but if the Kindle book has Real Page Numbers, so much the better.
And calibre has a feature to automatically generate a pseudo-random guesstimate apnx when sending azw3/mobi to a Kindle. This can be refined by using a custom column containing the page count (most likely derived by hand from checking the paper version). If used, the Kindle book should have pagenumbers as well.
I hope this helps you come to a better idea of what you want. Please note any Kindle proselytizing/promotion/bias is entirely incidental.