It wasn't John's stature or looks that had Omni assuming he would bottom. It was his humanity. Omni had been taught his superiority to humans was so evident that he expected them to bend to his will. The fact that they usually did only emphasized that to him. Of course, some people needed more persuasion than others. With John he hadn't needed to use any mesmerism or such. The man was completely on the same wavelength for what he wanted.
He was impressed that John could pay attention with all the sensations he was giving the other man. It made the game that much more interesting. As did John bracing against the desk. Omni smirked around the man's cock. Physics were simple. He let his hands drift up to grab John's arse. Then he simply pulled the feet out from underneath John while releasing the man's cock with a pop. It took a bit of strength but he was a bit stronger than the average human given his timelord physiology. As John started to fall he quickly pushed up and back.
John's back scraped against the desk as he was forced onto the surface. Omni rushed forward with a growl to slam the man down on the desk as he stood between the man's legs. With his hands on the man's shoulders he moved in for a deep brusing kiss. His hips thrust forward brushing their cocks against eachother.