You're making some assumptions which I think aren't helping what could otherwise be a good discussion between us. I was not attempting to take any control over how he spends his time. From what I recall, my statement to him about showing up late was in the vein of "We'll still be ending on time, so since we started late today our session may seem somewhat brief." It was from this kind of overt admission of the facts that he responded negatively. Now, given that this was about two years ago I cannot tell you verbatim what I said, but I do recall the overarching point I was making, and it certainly was not one of telling him what he should or should not do with his time.
I do, however, have boundaries. Showing up late by 20 or 30 minutes may be too much and I may refuse to see the patient for that session, and will ask them to reschedule with me. Even in such a case I wouldn't spend any time telling them how they should have been on time or asking where they were or why they couldn't make it in on time. Certainly, patients often will volunteer explanations for why they show up 5, 10, 15, etc. minutes late, but they do so without me asking them about it.
Having been a patient in psychotherapy myself at different points in my life, I can relate with the patient perspective. I've shown up late to sessions and had to cancel and reschedule before as well. From this point of view, I do know that people have lives and that the patient sees their time in therapy as "their" time -- not necessarily, as you put it, as a joint venture. Fair enough, but I think you're assuming I took issue with this aspect when I did not.
For me, the priority -- or the big picture -- is to accomplish two things. 1) Provide a healthy therapeutic context where the patient is encouraged to be introspective and to grow; and 2) Assist the patient, per the AAMFT Code of Ethics, with understanding the choices he or she makes and the implications of those choice, all the while being sure NOT to make choices for the patient or to encourage the patient into making certain choices (which requires a constant self-monitoring so that I don't push my personal biases onto the patient).
I don't see how a comment such as "We'll still be ending on time, so since we started late today our session may seem somewhat brief" takes away the patient's right to choose or puts any shame on him or pressures him into making this or that choice. It was a comment that was in the vein of, "You made X choice, and due to that I am now making Y choice. I just wanted you to know." My comment honored his right to choose how to spend his time and secondarily reminded him of my boundaries by saying we'll still be ending on time. That's all there was to it. I think this shouldn't have caused anything more than a minor -- if even a minor -- rupture in the therapeutic alliance, considering we had met at least a handful of times by that point.