How to have apple iBooks or Kindle synced between devices?
Put all you PDF in iCloud and they will sync everywhere.
Kindle doesn't play with iCloud or AppleID or iBooks in iOS 14 or earlier - nor on Mac.
Your best bet is to have kindle sync the content you got from them only and have Apple sync the content you choose to purchase and store in Books and iCloud. (Like PDF libraries and such)
There’s no technical reason Amazon doesn’t use Apple API. It’s just platform, business, privacy, control issues from what I can tell as a developer with access to the API and design docs on Apple side. As a consumer, I am steering more an more of my purchases away from Amazon since their walled garden doesn’t work for me as well as Apple’s walled garden. I love O’Reilly subscription as well so I’m mostly content to let Amazon be Amazon and use a physical kindle when I can’t get what I need elsewhere. I rarely use the kindle apps on Mac since they just make me sad and frustrated, tbh. I don’t blame them (Apple or Amazon), I just use the paper white kindle for what it’s great at and the iPad for what it’s great at.
All my PDF are in iCloud now and those I need a proper reader, I open in books or another third party app if I need to mark them up or organize them more rigorously than iBooks allows. Most I read out of the files app in practice. I never could get Kindle to work with my stuff. Perhaps someone else with years of trying has a better approach. Maybe I can learn a better way like you are asking.