There is another thing to consider...
Left/Right page margins in the epub css can be set in @page and/or the body css. If non-zero margins are set in both places then they should be additive e.g.
Code:
@page {margin-left: 2pt; margin-right: 2pt}
body.calibre {margin-left: 5pt; margin-right: 5pt}
should result in 7pt L/R margins.
I'm not sure, how the Kobo is applying its page margin setting. Is it overwriting the @page or the body css. Or is it possibly
adding to one or the other?
If you want to add top/bottom page margins then the only effective way is to use the @page -- but it doesn't look like the Kobo lets you use the slider to change these. I think you'd have to hard-code it in the epub, either manually or using calibre. Even then I'm not sure whether the Kobo would overwrite the values with zero.
I can't test at the moment as my PC is too flaky to use for long periods.