I believe the answer to this is that rclone and Google's webGUI does this process a bit differently.
Google just changes some permissions on the files so they now belong to your personal drive.
Rclone actually moves or copies them - and this is going to use quota.
I don't believe that Rclone can replicate this spesific thing yet. I don't know if Google have exposed the functions required to implement this. @ncw probably knows the details of this.
Within the same drive rclone can move stuff easily of course, but across different drives it can not yet do what the Google webGUI natively does yet (to the best of my knowledge) without requiring an actual transfer operation.