@Nick,
That isn't what the patch called `Margins fine tuning` is for. Left/Right page margins should be able to be set using the Kobo's adjust Margins slider. If nothing happens when you slide it, it suggests that particular epub's internal css contains left/right margins which are overriding the slider. If you remove them (and I mean remove not set to zero) before transferring to the Kobo, all should be well.
If you're a calibre user you may need to revisit your Preferences for Page Margins and set them to 'No margins' for future conversions. Unfortunately, if the left/right margins are already set in the epub, I don't know of any way other than manual (Sigil or calibre Tweak Ebook) to do the removing.
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