Remove the rear wheel and measure the rotor thickness (best done with calipers or 0-1" OD mic). Should be around .070" (1.8 mm) depending on the brand and amount of wear. Then use feeler gauges that stack up to about 0.005" less than the rotor thickness and insert between the pads. Then pump the brake lever a few times to set the pistons a little farther out of the bores. Re-install wheel and check the lever throw. Repeat as needed with less feeler gauge thickness until you get the lever throw where you want it.

If you go too far, just push the pistons all the way back into the bores and try again with a little more thickness to the feeler gauges.

I just did this a few days ago with my rear Guide R caliper. I do this procedure any time I bleed or replace pads/rotor on my brakes. I am very particular about my lever throw. It works for any open reservoir style hydraulic brakes, Shimano included.

Disclaimer: You always want to make sure the pistons on each side of the caliper have about the same amount of piston exposed to keep the caliper body centered around the rotor, otherwise you could end up with the rotor rubbing on the caliper body, even thought the pad to rotor gap is even on both sides.