NO! That is not normal! I have a FP Whipple which is basically a Whipple Stage 1 gen 5 and I notice no additional noises. The rotors do have an Abradable Powder Coating (APC) on the gen 5’s and I’d be willing to bet the gen 6 does too. The APC is designed to wear slightly against the housing to form a perfect seal over time. It can produce a slight rotational squeak on startup until things heat up (expand). I highly doubt that has anything to do with your noises. That rotational deep knocking sound alone is concerning to me. Like Davidwnuc said, contact Whipple asap.
Your installer is an idiot. That is NOT normal for a Whipple or ANY 5.0 to sound like that. Take it back and make them make it right and then NEVER use them again.
As others have said, that is not normal. I have a stage 2 and it’s not noisy at all at idle. I have seen a video that was similar to yours and Whipple said the rotors were not timed correctly. He had to send his back for repair.
I agree with the others. I have 25K on mine and while ive had a few mystery squeaks and squeals to contend with ive never heard that kind of sound from the SC. Hope you find a resolution to this.