I'm having the same problem described above, azw3 covers look very small in Paperwhite 5.3.3. Moreover, mobi covers doesn't show (even using the Facebook mark), that's how I passed to azw3.
I have a Touch and a Paperwhite, in the Touch everything is OK (mobi covers and azw3 size) but in Paperwhite just the opposite.
What is more strange, during the trials with Paperwhite there's one book that works the opposite, only mobi cover shows, and when I load the azw3 format, the cover is shown just for a few seconds, and then the standard cover takes over. It seems there's an internal process in the Paperwhite's start up that makes things difficult.
Very strange, isn't it? Anyone managed to solve this?