One reason to use calibre was illustrated to me recently: Sony has basically left the US market, at least for its newest reader.
For me, that means a move to another ecosystem. calibre has allowed me to convert the epubs and Sony format books I own for use on Amazon's hardware. Without calibre, my Sony formats and epubs would be inaccessible to me once my Sony hardware dies.
For you, not using calibre is perfectly fine, but it comes with the disadvantage of being stuck in Amazon's formats when their market undergoes a major change - as it certainly will in time.
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