I refuse to accept that as fact because 1: that is merely their interpretation, not the word of Nintendo (and by that I mean the company who re-developed the game for 3DS and got Nintendo's approval, not Nintendo themselves), and 2: Many Zelda fans are meticulous of our inventories, and the two extra spaces make us feel better.
This can easily be seen when playing games like Resident Evil and we spend a good few hours over the course of the game organizing our briefcases. However, in this sense, since the new inventory screen has no direct sorting, instead of having to make a dozen switches back and forth to change out one item while we also want and keep all of our not-currently-equipped items sorted the way we want, we have two spots perceived as "extra" by some that are there, in fact, so that we can always have a logical place to "put" our item X so that we have a free hand to then equip our item Y (since Jabun knows we're not magically inclined to make them teleport to each other's places instantaneously).