I was always under the impression that it was something mixed into the batter. Something maybe oil-soluble, or some of which rose to the top as the batter sat in the oven and settled just a little bit, and cooked into a separate layer, and some of which stayed mixed into the rest of the batter for additional sugary, chocolatey flavor.
Part of the reason I thought this was the differences in color and texture from the brownie to the flaky top (especially clear in box pictures). Part of it was the way it seemed to flake away from the brownie - after all, browning on the top of bread or other baked goods tended to match the texture of the rest more closely, and be really attached to the interior, not flake away.
KatieK's accepted answer on how to make the top crust flakier mentions it's actually a meringue (I have no other citation, sorry). Maybe a bit of meringue powder in the box mix would create that effect, if it is light enough to rise through the batter - and since it's egg white and sugar (and cornstarch), any left in the mix that didn't rise to the top would simply be absorbed into the sugar and egg already in the recipe. Somehow I don't think the white of the added egg reacts to the sugar on its own, since I don't see the same kind of crust on other baked goods.
If its not that, it might be the result of adding just a little too much oil, on purpose, because maybe a sheen of extra oil rising to the top will react with the extra heat and the batter below to create that flaky layer. Again, not saying that's what it is, but that if it isn't, I don't have any idea what else it could be.