First, the IBSZ is to zero the sights at 50 yards for the flattest usable trajectory. Period. End of story. Aint got jack shit to do with what type of sight you use. Aint go jack shit to do with elevation marks on the rear sight. The instructions about setting the sight to bottom out at 8/3-2 or 6/3-4 only apply if you are using an A2 style rear sight and want the elevation markings to be accurate.
About your question, apply a little thought here. As you already know and have already stated, the only difference between your sight and a standard A2 sight is the aperture. With that in mind, what difference could there be except the obvious one that the POI doesn't change when you flip the aperture?