I don't think clocking is transphobic, though I am 100% sure there are people on the internet who would argue it is. Like you said, it's aautomati. I can always tell someone's sex, and from what I can tell that is true of many women, especially when it comes to looking at males.

Yes, it's transphobic. You're revealing that they are trans to the outside world, which can put them in danger. And no, you can't always tell one's sex, you can only make educated guesses. Aren't you sure you're just seeing people that you know you're trans as their sex?

A lot of "trans" people think they pass because people lie to them about it. Check out any of the selfie or passing subs and you will see people who look unmistakenly male being told they look just like a woman or vice versa.

Yes, they all look to me like a woman. I can't tell that they are male. You're wanting to perceive those people as who they are not. I'm certain that transphobic people would tell I'm not passing (despite no one having caught me yet) if they clocked me as a trans woman.