If I'm following you correctly, no, Zentyal won't become a service on a running Ubuntu server. Zentyal is a management and integration product for Ubuntu Server, so Zentyal is "in charge" of all services it manages and integrates, not Ubuntu Server.
That leaves open the possibility that Zentyal could change the configuration of an already running service. Off the top of my head I don't know for a fact that it will change the configuration of an existing service if you add only the mail server through Zentyal. But I am a cautious sort of person and would want to test it out thoroughly before committing the idea on a production machine. In other words, it's not a typical use of Zentyal to use it in the way you're describing, if I'm understanding correctly.