If the piston is not flush with the body it's not completely compressed.
Try putting the caliper on the stand with only the inner pad and no slide hardware. Like this the caliper will be very loose, put a large screwdriver thru the hole in the back of the caliper between the rotor and caliper. Now pry itso you're compressing the piston, don't jerk just slow steady pressure. I've done this for years on my calipers and never had a problem getting the pads in afterwards.