I was in a similar situation, having recently bought a Kindle PW, and also reading on Android phone & tablet kindle apps.
I found that I can
- upload a .mobi to each device with non-Amazon-cloud tooling (e.g. calibre usb upload, dropbox download, etc...). The page syncing would work with whispersync, but not the syncing of notes/bookmarks. The book was marked as a book though in the PW
- upload a .mobi to each device via 'email-to-kindle'
=> full syncing of pages & notes
=> but the PW shows it as a personal doc.
I prefer the 2nd solution, for the full syncing.
I understand you're on iOS, not Android - I dunno if that is gonna give you all different user experience from the above.
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