Yeah, Kobo's site is a little goofy with picking a default format for you. I know I was able to download a different version once, I forgot how I got to the option though.
I'm a big fan of Calibre, so I download everything in ePub so I can load and manage it in there first. Then I have a simple Applescript workflow that adds new .epubs into iTunes for me. iTunes organization of eBooks is pretty bad, ok, it's very bad.
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