Pick the mounting style that works best for you..
Over-Mount Style: Overlaps the backer-board by around 1.5" on every side, and provides more flexibility on your cutout. The flange does contribute some thickness, and needs to be feathered out with thin-set.
Flush Mount Style: Wall cutout has to be more precise, however there is no need to "feather out" the edges for a smooth transition. Silicone caulk is used to seal between the niche and backer-board edge. A narrower flange allows closer placement to the corners.