Much like increased stride length is an indicator of higher velocity, simply extending stride length by reaching with the front leg doesn't really help a pitcher generate more velocity.
The tendency of people using the towel drill, when not monitored by a competent pitching instructor--and in my experience most are not competent, is to reach with the arm to get the release out front and snap the towel onto someone's hand. To achieve this, most will bend forward at the waist earlier than proper throwing mechanics would dictate and the students get out of good posture just to get the hand out there. Employing the trunk flexion too early and engraining that pattern reduces the effectiveness of trunk rotation by cutting it off too early. Cutting short rotation at the end, where it should be translating into the biggest velocity gains, seems counterproductive to me.
The towel drill, done with improper supervision and correction, reinforces this early upper half, which your son definitely wants no part of because he's already too early with his upper half. In my opinion, improperly using the towel drill will make that impossible to correct.