The holes are the rivets that hold the two pieces of Kydex together. I think the two piece sandwich enables them to make the whole thing thiner at the sides (front and rear of the gun). They are nice heavy rivets, and look to be very well fit and seated. May be a source of weakness, so I will inspect regularly, but rivets do hold some high tech stuff together don't they?
The various belt loop and hanger thingies then screw through the revets- Raven spaces the rivets to allow additional pieces like mag carriers and light holsters to then also link up via the same screws. Hence they call it a system.
To answer your question, the holster challenges concealment by adding thickness. Leather and double leather, thick kydex, clips placed over the holster all add thickness to the Rig. What I think Raven does well is use thin kydex, and ensure the edges along the front and back of holster (leading and following edge) curve to the body, thus reducing the overall size of the blocky thing. Leather does this really well too, of course, but I am kinda a kydex guy for this gun and EDC. So to me it is a good choice- so far.