I'm no infantry guy or anything, but when I was in Afghanistan, everyone I saw carried mags top up in their pouches, I believe. Although now that I think of it, that wasn't the case for my pistol mags... but I think that's more a case of "how would you load it". Pistol mags are usually either stored on a shoulder holster (in my case, almost always) or a thigh holster, so the way you'd pull them out means it would probably be more convenient to have them top down... does that make sense?
Whereas assault rifle mags are usually stored on a tac vest of some kind, or right around the belt area - you pretty much want to be able to take it out and have it go right into the rifle, which would be "above" where the mag pouch is, usually. So top up.
Yeah, even in a non tactical situation, the dust gets everywhere and piles up in the bottoms of mag pouches pretty quickly. You don't want to have the open end of a mag sitting in that crap.
Probably not the best explanation I've given - like I said, I'm no expert, but that's just how it's been in my limited experience.
I think Sideshow's way is just a compromise between having a proper 1/6th scale mag pouch and realistic magazines that fit into 'em. They might look too big if you were able to get them in bottom first.