One of the big advantages to throwing is that you can throw quickly, even if your arms are full. Fighting off a horde with a fencing and a rapier and there’s a spitter approaching? No problem, just chuck some rocks at it. Don’t have to drop your weapon, don’t have to pick it back up again, you can just throw rocks while performing fencing counters against anything that attacks you.
But if you use an actual ranged weapon, you have to drop or sheath the rapier, draw or pick up the ranged weapon, aim, attack, and then change back to your rapier (dropping or holstering the ranged weapon in the process).
It gives throwing a huge benefit over other ranged attacks.