I got the same brakes, and a similar problem. I believe the inner pads of both my front and rear don't retract as much as the outer pads.

Try this trick:

1. Start by pushing both pistons as far as they will go into the bores.

2. Mount the wheel/disc rotor.

3. Loosen the caliper.

4. Place shims between the rotor and pads. If your inner is not retracting, place a thicker shim on that side. I use a business card, or one of those fake credit cards (or hotel room key).

5. Squeeze the brake levers and hold them, then tighten down the caliper mounting bolts.

Hopefully, this will both center the caliper and maintain enough clearance at the pads.