the roughness depend on the substrate (the type of silicon, predominant direction) and the vacuum inside the chamber. If there are good condition achieved you can get roughness less than 5 nm.
In case of thermal oxidation using dry O2 or vapor oxidation rate depends on substrate temperature and the supply rate of the oxidizing species to the interface between the Si and SiO2. So, to achieve as homogeneous silicon layer one has to keep these two parameters constant through out the surface of the wafer.
So the fluctuations in the thickness of the oxide depends on controlling the homogeneity of these two parameters.