Pistons are aligned only without pads in I've reset the pistons (after taking the pads out) of my XT hydraulic brakes, and made sure they do extract evenly when operating the lever.
After putting the pads and the wheel back in (and adjusting the bracket mount to a symmetrical position over the rotor), the left piston extract much more than the other one, which was the reason i wanted to reset it in the first place.

Any ideas why?
If the pistons extract evenly without pads but uneven with pads, one of the pads is giving more resistance. Try to clean the whole inside of caliper and check the pads and how they fit inside..