I agree that I am lucky to get a Ph.D and a position after I xxxxted a manuxxxx without his knowledge. After I confessed to him, we were working in the same direction for a fruitful tomorrow. But the Ph.D candidacy exam really pissed me off. It was my fourth year and I had put more time on the experiments than on the candidacy exam in the previous three years. When he insisted postponing my candidacy exam after the publication incident, what I thought most was when or whether he would let me to get a Ph.D. My struggle at that time seemed to lead into the wrong direction.
For my post-doc job applications, some interviewers told me that my Ph.D. advisor wrote me a good letter, and when I told these interviewers that I xxxxted a manuxxxx on my own, they were all shocked. However, some interviewers did either directly say or indicate that my Ph.D advisor gave me a not good reference or even no reference at all. My first post-doc advisor showed me one of my Ph.D's reference email, and from there I did know that he was trying to prevent me from getting a job.
I hope that my experience would not be repeated on some newcomers, because it is a common thing for a graduate student to send out manuxxxxs for publication together with the boss's name.