I can't find a statement in the media overlays spec that the total duration for a publication has to equal the sum of all the individual durations for each overlay (it's not in the packages spec, either).

It's true for audiobooks, and how the total is calculated in the NCX, so I can only assume this should be true here, too. epubcheck doesn't currently test this, though, and without a clear statement it's hard to justify adding it.