Lesser impact to the ground
You are essentially jumping on the tips of your toes to also work the calves. When running, you are going ball to toe which is more stress on the knee joint and shin bones. Even if you adequately stretch, you will still experience some discomfort if you run for long periods of time.
You can reduce this by running sprints or just reducing the distance you run but you may still experience discomfort.
To me, even when I do knee raises/running in place while I jump rope, I feel I have more control over the cushioning of my impact to my feet vs running. When you run, the key is to try and develop a rhythm. It's kinda hard to do that and still concentrate on cushioning your impact
Just my .02
