Simple: becase it isn't possible to follow step 1 with an ARMS #40, which is required in order to get the proper zero using the SMALL aperture.
The standard A2 aperture is designed so that the center of the small aperture is higher than the large aperture. This is a GOOD thing, and proper for the design of the sights. It is also vital that you understand that when you flip the aperture, you are changing your zero.
The IBZ proceedure directs you to click your sight down two clicks, then zero with the small aperture. The clicks are to compensate for the height difference between the apertures, and to allow you to use the small aperture, which is easier to shoot with precision than the larger one.
Because the ARMS #40 doesn't have elevation adjustments, you can't do this, and must use the large aperture.
Once you are zeroed with the large aperture at 50 yards, you use the large aperture for anything between 0 and 250m, and you'll have a very flat trajectory that stays within 2" or so of your point of aim out to that distance. To shoot at 300m, you flip to the small aperture, which changes your zero to 300m. Now, normally, on an A2 sight, you start using the elevation wheel to adjust elevation for targets beyond 300m. This isn't possible with the ARMS #40, so they've cut the top of the aperture off and notched it to make a 600m sight. Anything in between must be estimated. However, given that these are BACKUP sights, the chances of you EVER using them to engage targets in excess of 300m is very remote anyway. 99+% of the time, if you've gone to backup irons, your problem is close to you, and you'll be using the large aperture.
-Troy