This "windup set" will be slow to the plate, even combined with the slide step. It has to be, as the body must rotate. In the stretch, the shoulders and hips are already properly aligned.
If using windup & stretch is a problem (e.g., too much variation), then a pitcher can throw only from the stretch (as some do).
The different slide step mechanics do violate the KISS principle. And from that standpoint there is an inherent problem.
Flail and arm slots are not linked. Pitchers can flail and use any arm slot.
Regarding your study, correlation does not mean causality. And again, all you have to do is feel it yourself. Even with no flail at all, a person can feel greater stress in the rotator cuff and triceps when taking the arm back fully extended as opposed to arm circles. I certainly can feel it. Have you tried it?
What you are describing in your response to the inversion is the "overhead" slot (arm fully extended up to the sky). Not the "overhand" (upper arm parallel to the ground, foream 90 degrees to the ground).
The overhead slot is very stressful on the shoulder. I can't think of a young pitcher I coached who used the overhead slot that didn't have shoulder pain. I always advised them to go to overhand. The ones that went from overhead to overhand saw the pain go away.
And yes, there will be a greater down angle on the pitch. But there will be less horizontal movement on the ball. The overhead pitchers I have seen tend to throw straight & flat. This is easier to hit, even with the added down angle, compared to the pitches from other arm slots that may have slightly less angle but significantly more movement in the horizontal plane.
And with regard to where the forearm is at release, many pitchers use the three quarter slot. Not even overhand, much less overhead.