[tomsem]

You can use custom fonts with azw3 (for sure), I think embedded fonts as well.

No page flip or ligatures.

PDF does allow annotations. They just do not sync to other Kindles and Kindle apps.

I keep waiting for them to start delivering Print Replica instead, which would support annotation sync. The Kindle apps, along with Scribe, get Print Replica, and do sync annotations (highlights, text notes and bookmarks) and reading position. The apps do not yet show Pen annotations made on Scribe.

All of the Kindles which are running this version (and for several versions before) can render Print Replica if you go to the trouble of making one and side-load it.