There are several reasons to clone a PCR product but the main reasons include expressing the product and maintaining the library inexpensively.
In the study you mentioned, the cloning and transformation is apparently done for obtaining single clones (from single colonies).
Clones were picked randomly and colony PCR was then performed using
No enzyme is involved in base-pairing (annealing).
This does happens by chance, but the chances are governed by stoichiometric considerations.
The main such consideration is that the (low molecular weight) primers are added at a high concentration (greater than that of the DNA) and therefore have a greater chance of encountering the appropriate region of ...