Nikon D5300 focus noise?

Nikon D5300's makes a weird noise when autofocusing. Does it do this with the VR II lens? Or only with the VR I lens

It may do it with only one specific lens.

One reason is that each lens has its own focusing motor, and noise levels vary.

The D5300 does not have anything to do with autofocus and whatever noise comes from that since it has no focus motor. That's in the lens so if you think there's something wrong with yours, try out another copy of the same lens and compare. If you are bothered by the noise of your lens, bring it back to the store you bought it from with the sales receipt and ask them about it.