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In defence of Kobo... I'm relatively new to Kobo world but can categorically say that calibre-sent standard epubs render margin-top/margin-bottom (as contained in internal epub css) perfectly.
Kobo allows user configuration of Line Spacing (line-height in css terms) but will override with the epub's own css, if present. Unfortunately the Kobo minimum setting for Line Spacing is rather larger (1.3) than many would probably prefer, so this could be an issue.
If you want to selectively change paragraph top/bottom margins the only option is to roll up the sleeves and surgically edit the relevant epub css classes with something like Sigil or calibre Tweak book. Unfortunately there is no automatic magic button called 'make my epub perfect'.
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