If I might jump in here, I think the key point in the discussion is what does night fighting actually represent? Giving a unit stealth or shrouded based on their distance from the weapon doing the firing is a way (in game terms) of making it more difficult to hit because it's dark. So if you've got the shrouded rule from being more than 24" away, what they're actually saying is that despite the target models apparently being under the blast template, there's a 1 in 3 chance that they're not, because as it's dark you can't guarantee your shot is so accurate.
GW could have dealt with it by any number of other methods, like adding an extra D6 to the scatter for stealth, and 2D6 for shrouded, or reducing the firer's BS, but instead they decided to use a save. In fairly typical fashion, it's fuzzy rules writing, by using the stealth and shrouded rules, which are phrased as cover saves.
In short, don't think of it as a cover save, think of it as an inaccuracy penalty for shooting at a unit you can't see properly.