Two related illegal pitch questions

[SC Ump]

NFHS:

Upon return of the ball to the pitcher, she will "practice" her rotation before taking position on the pitching plate. She is in the circle and does her windmill motion, sort of pitching the ball into her own glove, like she is loosening up. This is fairly common, at least in games around here. Illegal pitch? I have never thought so.

Situation yesterday: R1 on 2B. Throughout the game, the pitcher was doing as stated above. After one pitch, the catcher returns the ball to the pitcher who then "takes a moment" while standing about 2 feet behind the pitching plate. She pauses while looking at the ground, takes a breath and just relaxes. She then looks up, and does one of these "practice rotations". As she does, R1 apparently things she is delivering and "flinches", but before stepping off 2B, realizes it is just a practice rotation.

This raise a lot of questions in my mind about what to do if the runner had left the base by a step or two. I could rationalize it as legal by saying the ball was out of the pitcher's position for a fraction of a second while the ball went from her bare hand to her glove. But then what should be done if the runner was stealing and got caught at third.

It would almost make me think this common "practice rotation" should be considered an illegal pitch. Our at least if it is done while near the pitching plate when facing the catcher.

Thoughts?