Why were clocks considered to be models for the physical universe?
The clocks moved around in order and had regularity in their way of functioning. Just like the clock, the universe was considered by many scientists like Kepler and Boyle to be a giant clock in which everything moves around in perfect harmony with each other.
Like the clock is developed by humans, similarly the universe is created by God. Who has set the entire natural processes in the universe on its own course. The basic idea is that just like how a clock works in rhythm, the universe also functions in the same manner having precision, regularity, and predictability.
For psychology, the path was cleared by the automata and clocks. Even humans could be thought of as machines or clocks as they are also governed by the same physical laws of nature.
Their body functioning resembled the machines. For example, the animated flute player was designed like a human. The wires and springs, corresponded to a human body part. So, by this analogy the actual human body can be thought of as a machine or as a clock. When the clock is set in motion it operates like the human body, which designed by God. Both move in perfect motion as they are designed to move in.