I've blown out many a master cylinder by depressing the caliper to fit the new pads in thus creating back pressure that can defunk the master cylinder. I always open the bleeder on the caliper while depressing. This saves me the hassle of explaining to the customer wy they need a new master cylinder when they came in for a routine pad change. If you close the bleeder while depressing just before you get to the end of the travel there's no need to bleed the system.
paul