Perhaps you've already recognised, as I nearly did, that 'Godot' originates from the play Waiting for Godot, which portrays the scenario in which two characters wait, in essentially the one place, for a mysterious person named Godot that never arrives. Thus a Godot machine is a mechanical device that keeps a subject of interest in once place at all times. In Ollie's and Physical Virus's case, the subject is an ant.
Godot Machine 1.0-1.5 from Ollie Palmer on Vimeo