The pistons always stick out a bit, they automatically adjust for pad wear. That pads hardly move at all, each pad only moves about half a millimeter anyway. (On a Mono Trial, on a Mono Mini the leverage ratio is smaller, so the pistons should move further in theory anyway). If there is a little bubble of air trapped in the system, I've found that it doesn't matter, it moves up through the brake as you use it, just check that the diaphragm hasn't got any air under it or it can move into the hose if the bike ends up upside down. To get the sticking piston out, hold the one that's moving into the caliper with some pliers and gently pull the lever, you'll probably find it will suddenly let go and become free, apparently this is because the seal ends up drying out and sticking to the piston, in my experience it always happens on the inside piston, closest to the hub.