Some people will add the agent to the golden image while others might choose to add as a run once or first boot after the VM configuration. For the agent, it is just a service that gets created so you have some flexibility where you could add the files to a hidden folder and access when needed if you are doing other deployment outside of vCAC or if vCAC is the only deployment method then you could install and add it as part of the image.
Options are good and you have some!
Steve