I believe those are anti-squeel plates and I would suggest leaving them in, after figuring out why you have such little clearance on the pads. Are you sure the pistons are retracting fully into the calipers? There really should be enough clearance there even with brand new pads. It's possible that there is some build up on the pistons that is preventing them from going back into the bores fully, giving you the clearance needed. Maybe try gently pushing them in further, e.g. by placing a large screwdriver between the disc and the pads, then twisting just a bit.