The Supreme Watchmaker is, according to the beliefs of the Church of Besainted Pelagius, a deity providing "divine inspiration" to Pelagius himself. Through the Watchmaker's "temporal presence", all of Pelagius' technology is considered holy.
According to Pelagius, the Terran Confederacy also possessed knowledge of the being, fearing the scope of Pelagius' own knowledge and hence sending a ghost agent to terminate the movement (said ghost failing and becoming indoctrinated).
The concept of the Supreme Watchmaker may be a reference to the "machine god," inspiration, which may have been taken from the concept of Deus Ex Machina - the "God from the Machine." It could also be a reference to the "watchmaker analogy" for the existence of God, popularized by William Paley.