I'm a Calibre user, but 1) I don't like to have to physically connect my device every time I want to sideload a book. 2) I've not found a single CSS setting that works for me in every book.
So my current workflow is to tweak a book in Sigil, look at it in Adobe Digital Editions which renders very close to the Kobo, then copy to a folder on my server. Then I download at my leisure via the browser on the Kobo.
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