Kepubs have a more pleasing structure to them (and they may be a bit faster) so if you sideloaded using Calibre there's a plug in you can install that authomtically sends epubs to the kobo as Kepubs. I can't think of its name right now but I'm sure someone will be able to point you in the right direction when you want to install it.
It doesn't affect the ePub in Calibre at all, just sends it to your kobo as a Kepub.
I have had my Glo HD since Monday and it's fine, speed is fast enough and I'm enjoying reading on it.
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