I agree the central problem is the lack of a standard protocol for managing metadata like this but not that there are few with my needs. All the "human" ebook readers I know, at least those who study ebooks and not only read them, have told me at least once: "The ebook reader is cool but I switched from Kindle to Kobo and I lost all my annotations.." - ...Cool but I can't see highlights of sideloaded epubs on my pc..." - "...Until they will not improve annotation/highlights management I'll go on with paper"...
Anyway, what I wanted was to have a clearer and up-to-date idea of what is possible right now regarding this issue. If there should be any news I hope someone will come here and say it. In summary:
- As for ereaders devices like Kobo or Kindle, cross-platform syncing of sideloaded ebooks purchased outside of their stores is not yet possible.
- As for mobile apps, the only ones I know that have cross-platfrom highlights/annotation sicronization are: Google Books, Pocketbook and Fbreader (at least according to what Fbreader says. I tried it and it doesn't work).
- A DIY alternative is to install on pc mobile-only apps, with at least cloud sychronization of annotations and highlights, using android emulators or Windows Subsystem for Android. I am currently using this trick with Moon+ Reader Pro with much satisfaction and I consider it the best and most efficient solution for me at the moment.