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Okay, to answer your second question first, yes, you can using calibre.
As to the first question:
store bought kepubs will sync across devices as will the annotations you make in them.
They also provide added reading stats pertaining to how many chapters, length of chapters, how much time to read the current chapter, the next one and the book.
The presentation of kepubs is different than epubs but it's a question of personal preferences.
Books converted to kepubs will provide you with the same layout as storebought kepubs but won't sync and won't provide all the added reading stats (at least with newer firmwares, they could with older ones).
There are also epubs that automatically download/sync to your device, these work the same as kepubs to be honest.
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