Make sure I'm clear here. An inverted nipple is just a standard nipple, flipped upside down inside the wheel? I can see why that would be PITA.
it varies from manufacturer to manufacturer, but yeah, that's the jist of it. usually, it's not a standard nipple, but whoever happens to be making the wheelset's proprietary flavor of the month nipple shape and size, for which you need the manufacturer's proprietary flavor of the month tool for. for instance, campy wheels use a slightly larger nipple than Bontrager (talking about the super aero carbon tubulars here), but they're both Hex (i think campy uses 6.5mm, and bonty uses 6mm or something ridiculous). FSA uses a square shape, i think.
at any rate, the design is stupid. they are difficult to maintain, which leads to surly/lazy mechanics. as mentioned before, they don't offer any kind of percievable advantage.
although, i think i'd rather true one of those wheels than the god awful shimano wheels with the nipples at the hub. don't get me started on those...oh, and the dura ace wheels are supposed to be tubeless now, which just adds to the chuckle/pointless factor.