You raise many good points, but you overlook one important dimension — timing of exercise. Exercise can reduce postprandial glucose levels. Whether or not this translates to better overall disease outcomes remains to be properly tested (only small studies to date that I can find). However, there is at least a plausible mechanism given that postprandial glucose levels correlated with elevated levels of glycated hemoglobin (HbA1c). It may be true that, as with so many things in life, timing is everything!
This article provides a good perspective: