#Thinking about this alongside all of the other significance that people calling Minkowski Commander takes on:

[hephaestuscrew]

I'm sure Minkowski never forgot that Cutter was the first person ever to call her Commander. After recruiting her in Once in A Lifetime, he starts to call her Lieutenant, then breaks into laughter, before correcting himself: "What am I saying? Commander Minkowski." He draws attention to himself granting that title, stressing its significance. By initially calling her by a lower ranking, then conspicuously correcting himself, Cutter emphasises that he's the one granting her that title. Right at the beginning of Minkowski's employment with Goddard Futuristics, Cutter plants the seed for his line in the finale: "People cared about you because of what I made you: A soldier. A leader. A commander. I gave you that, and now? I taketh away."

And he does take it away. Cutter makes a point of calling her Commander in that first meeting, but he hardly ever calls Minkowski Commander after that. He almost always calls her Renée. He makes the point in that first interaction that he has the authority to grant her that title, and then in every subsequent interaction he tries to make the point that she doesn't have command over him. Having called her Commander once makes every time he doesn't call her by her title seem more deliberate. It's not that he never uses titles - it's that he uses them selectively. He gives her a taste of that sense of authority, but he doesn't want her to feel worthy of it.

In the liveshow, he cuts her off by shouting "I AM SPEAKING, LIEUTENANT!". Minkowski is the Commander of the Hephaestus in official terms at this point and Cutter even refers to her as "a mission commander" later in the same episode. So there is a deliberate malice to Cutter calling Minkowski Lieutenant here. Not only does it emphasise the use of authority structures as a means for control and the abandonment of first-name-basis false friendliness, calling her by another title makes his choice not to call her Commander even more explicit, denying her that authority.

Apart from when he recruits her, the only other time I can think of when Cutter directly calls Minkowski Commander is in Ep60, when he lays out his offer to let Minkowski leave on the Sol: "How does that sound to you, Commander?" Again, calling her Commander is a kind of power play, an attempt at manipulation, highlighting the sense of responsibility that motivates so many of Minkowski's actions. Cutter is prompting her to ask the question she would be asking herself anyway: what choice would a good Commander make? Just as he did when he recruited her, Cutter offers Minkowski something she desperately wants, and the use of her title here only draws attention to the idea that Cutter is the one with the power, choosing what to give her.