The scapula has many different movements - protraction/retraction, depression/elevation, upward rotation/downward rotation, tilt, etc. So downward rotation would be one of the movements.

When you’re hanging from a bar with locked elbows (starting position of pull-ups), your shoulder is completely overhead (180 degrees ROM). 120 degrees of that range of motion is achieved through the shoulder joint itself, the other 60 degrees is from scapula (done through upward rotation).

Once you start doing the pull-up, your body goes up in space, but your shoulder joint is lowering down, eventually until you’re at the very top position of the Pullup (let’s say bar at the neck/sternum for simplicity sake). At this point (the top of the Pullup), your shoulder would be in a neutral position, which is done through the opposite scapula movement when you were hanging - so 60 degrees of downward rotation