Bodyweight skills definitely have an upper limit, unlike weightlifting which is limited only by how many plates will fit on the bar, leverage can be varied quite a bit, increasing the difficulty of these skills. Progressive resistance makes you stronger. It does not matter if this comes from varied leverage, or extra weight.
Both bodyweight and barbell training will help you gain muscle but for example with squat you cannot add more resistance with bodyweight to develop raw power.
Also, its well established that for barbell training, if done correctly at high intensity, will stimulate more muscular growth than bodyweight exercises for the same muscle groups.
There are many stories of people who don't weight train and end up lifting very large amounts their first time out, due to body weight skills. Here is a video of Ross Enamait deadlifting 495lbs (at 170lb body weight) with no deadlift skills and a primarily bodyweight-only training routine.
Simply, it's going to take me too long to develop the strength to squat 495lb if I go down the bodyweight-only route compared to if I were to go down the barbell route.