No reason at all you can't use Calibre!
When the Kobo is plugged in, it appears as an USB storage device to the PC, and Calibre from version 0.8.7 (June 24, 2011) has had explicit support for it.
Certainly, there are currently some issues related to "Corrupt Storage" on the Kobo Touch that some anecdotally feel is related to Calibre, but Kobo is working on this.
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