Not a problem for me, because my sync is manual, not automatic. I assigned it to a gesture (tap the top-right corner): wifi on, sync, done. Waking the device doesn’t trigger anything, so I never get that “jump to latest position?” dialog.

I did it this way mainly for battery, I don’t want wifi turning on every time the Kobo wakes up. And I push my position at the end of my reading, so the server is always up to date and there’s nothing stale to pull next time.

I did think about auto-syncing when you open a book, but haven’t done it yet, partly for the reasons you mention. For now the manual gesture works well for me.