I just picked up my bike from the dealer today, although I didn't get a new bike all is well. For the front forks they took them apart and added more grease, that significantly improve the rattling. The little bit of sound I do here I believe is normal under heavy pressure. And for the rear brakes the caliper they had to remove some of the powder coated paint, all is good.
But I have to admit I'm not impressed with the overall characteristics of the front fork that is manufactured by suntour (SR Raidon 29" (Custom for Giant), Alloy Steerer, 15QR w/ Lockout, 100mm Travel). I had a low and giant mountain bike years ago that had a Suntour fork, and didn't like it. I thought with buying a better mountain bike I’d get a better fork, it's definitely better than the cheap fork on my cheap Giant but I still don't like the feel. So probably be replacing the forks soon.