When you think about it having the pistons all the way back into the bore makes sense. It reduces on of the places a bubble can hide. I would envision removing the old pads inserting the new ones and then locking the new set against the caliper. Maybe insert a taper like a screwdriver blade. When you are finished with that corner remove the taper and continue.
Don't forget the obvious, pump the pedal prior to driving off.
The only drawback I see is is when you spread the pads, you mash old fluid into the reservoir to mix with the new fluid. Being somewhat a purist, I change the pads on one side but do not torque the wheel bolts so that they are easy to remove when I come back to that side to bleed the brakes.