Nikon focusing. How it works?

I have a Sigma 100-300mm f4 but it has a focusing issue (not really a problem), when focusing it flickers minutely when focusing. It causes quite a few unfocused photos when I really needed them in focus. I shoot with a Nikon D5000 and so the lens focuses with the lens focusing motor as the Nikon D5000 does not have an in built focus motor.
My question is whether if I bought a Nikon D300 (inbuilt focus motor), would the sigma lens focus better.
Does the inbuilt focus motor over ride the lens focusing motor?

The auto-focus motor in Nikkor lenses are patented and third party lenses like Sigma and Tamron have to try to make their lenses work without infringing upon the patent of Nikon, Canon, Pentax, Sony, Panasonic, etc. That is the problem. The possibility that the D300 camera auto-focus would correct the auto-focus problem you are encountering when using your D5000 can only be tested with that lens mounted on the camera. To do that, you need to visit a proper camera shop and test your lens on a D300s that they have in stock.

The real problem could be that you specific Sigma lens is defective and needs to be replaced. I suggest you contact Sigma first before trying to change cameras

And NO. The in-camera auto-focus motor does not override the in lens auto-focus motor. All the Nikkor AF-S lenses have a vastly faster auto-focus ability, so when I attach one to my D300 or D3, those lenses perform better than the older Nikkor AF lenses when it comes to fast and accurate auto-focusing