Pull ups don’t require you to be lean. I don’t know where you got that from.
Your body responds to the stimulus you put it under. For example, if you lift heavy weights, your body has no choice but to build muscle in response to that stimulus. Well calisthenics works the same way. Because most calisthenics movements (i.e. pullups and dips) require you to move your body through the air in opposition to gravity, the body responds to this stimulus not only by building muscle but also by cutting fat because extra body fat is more weight the body has to lift through the air. The same sort of stimulus doesn't exist in weight lifting since those exercises don't involve lifting the body through the air in opposition to gravity.