Words matter. A good builder will discard a defective brick rather than incorporate it into a foundation. Words are the building blocks of thoughts, and sometimes it is worth considering whether the materials we are using are up to the task.
Consider the word "clocked". It sounds horrible. One gets clocked by a falling rock, a vicious left hook or an inattentively operated vehicle. The word carries emotional weight, implying an adverse, often malignant event.
Seeing the word so often used in the context of transgender social interaction, I have spent quite a bit of time distilling what it means. Objectively, it means that one is recognized as transgender. It may include misgendering, but does not require it--one can be clocked without being misgendered. Nevertheless, these terms are often closely related, and each should be considered in turn.
Misgendering is frustrating. Gender identity runs deep within our psyche, and transgender people, in my experience, tend to expend a good deal of ender in presenting or enacting their gender. Our internal coherence is rocked by incoherent public experience. Further, since misgendering may persist, it begins to feel like an picked scab. I hate being misgendered, and I hate the extent to which cis folk don't get the pain. Three things are certain in the trans life--death, taxes, and that your completely cis friend who was once misgendered from behind or in a dark room will say, "Hey, that happens to me too."

That said, misgendering is usually unintentional. People don't
want to perceive me as male. Subconscious processes make a gender determination long before they give the matter conscious thought. Sure, there are people who intentionally misgender, repetitively misgender or misgender out of ignorant commitment to the false equivalence between gender and birth sex. And, for me at least, I tend to respond to it differently. Being accidentally misgendered might make me sad, depending on the day and my attitude going into the event. Being intentionally misgendered makes me angry. Though it might hurt either way, intent really does matter.
This brings me back to "clocking". Again, it does not objectively mean anything other than that the person in question perceived the trans person as trans. People can, and usually do, in my experience, recognize that I am trans but keep it to themselves. Look at the sort of questions asked here: "Was I clocked?"
I submit that if you don't know, it really doesn't matter. And, if you know you were "clocked" (for example, if you are adept at reading the other's eyes and body language in such a matter that you perceive their perception), but nothing was added to it, it doesn't matter.
Unless.
Unless you think being perceived as trans is, in and of itself, an adverse event. Hey...been there, done that, but I'm over it. In the end, I decided that not wanting to be seen as trans feels just a bit too transphobic for my comfort. Think about it...when you see (i.e. "clock") another trans person, how do you react? Personally, I smile. My brother. My sister. Why should I take offense if someone else recognizes that I am transgender? I've thought about this question a lot, and I can't come up with a decent answer.
In my opinion, the word does more harm than good. I wasn't clocked. I was
recognized. Changing the language instantly creates a better frame in which avoid negativity. I recommend it.