The Omega-1-Nanite is a type of Nanite that Dr.Rylander had created. He then put in Rex's body. My guess is that he put in Rex for a reason. He maybe thought if Van Kleiss had ever came back,the Nanite could be used to safe Rex and get his other Nanites back. It can also make more Nanites if needed.
The Omega-1-Nanite kinda means a control Nanite. Based on what I've heard.