So, for example if you have a 100mm and 200mm macro lens, both with 300 deg focus throw, both get to 1:2 at close range - if you shoot the same subject at the same magnification (working distance is obviously different), then the focus throw to cover the subject will be similar (I think?)
I knew this was wrong... If for example, you focus the 100mm from 1 - 0.5m, and the 200mm from 2-1m, the focus throw will be the same over this distance (focal length and distances doubled, but magnification is the same). However, the 200m lens covers twice the distance (1m from 2-1m) compared to the 100mm lens (0.5m from 1-0.5m), so it focuses twice as fast for the same focus rotation. If you want to focus-stack a flower with 5cm depth inside that range, the 200mm lens will require half the focus throw compared to the 100mm lens.
So, if you need very slow, precise focusing, in general a shorter lens will give you greater control than a longer lens. On the other hand, the longer lens, with the narrower field of view, will give you more blurred backgrounds for the same DOF (or you can stop down more for greater DOF on the subject, with similar amount of background blurring as the shorter lens)