First, you mentioned chakra rotation. Now you mention chakra alignment. You need to get your facts straight. Anyway..
I had this experience, which was not exclusively meant as a chakra meditation, but it was part of it, where I used a crystal with a corresponding chakra. I was lying on my back, and as part of the process, I spun the chakra I was mainly working with at the moment. It was quite a good experience, so that is why I had to ask why, because I would like to see some reasoning behind such statements.