It is OK for the fairing's feet to rest on the sunroof/moonroof of your vehicle as the padded feet will certainly protect the glass from scratching. However, you will not be able to use the sunroof/moonroof with the Fairing installed as the feet must remain firmly on the roof of the vehicle. You will need to remove the Fairing in order to fully use your sunroof/moonroof.
If you have further questions please contact us here, or by phone at 888-925-4621 during business hours.