Absolutely, margin-top and margin-bottom is the way to go. Like I mentioned, earlier this year users discovered that Marvin for iOS misbehaved in this regard, they reported it to Marvin's developer, Marvin then got fixed, and it now handles margin-top and margin-bottom correctly.
I haven't encountered the flaw described by davire in Moon+ so far. Unless we take a look at the book's code, we can't be sure whether the misbehaving "change of scene" break is due to a Moon+ malfunction, or due to non-standard code inside the e-book. If the former, I would report the issue to the Moon+ developer.