I have experienced seals on a master cylinder being damaged (as mentioned before in this thread) by pressing the brake pedal to the floor during bleeding or by pushing the piston back in a caliper when changing pads and then disturbing something back up the line into the master cylinder. Granted, this was in the old days when the world was still black and white
Since then I always open the bleed nipple when I push caliper pistons back and capture the fluid via a bleed tube. When bleeding brakes I only ever press the pedal halfway down. Takes longer but never puts the master cylinder piston into a section of the cylinder it's never been before. Not had a problem in decades doing this.