Funny, I didn't see that discussion but FWIW, I use the word autopilot too, to describe what happens as someone first learns the squat, is trying to actively think about about 50 different things at the same time, which is impossible, and so does most of them poorly; to the time (usually only 2-3 weeks later, if they squat 3x/week) where all of those processes are happening without active thought, because they've been patterned, and the person can just think of the 1-2 primary things they need to do to improve their lift.
Your questions are somewhat poorly worded so it's not really clear what you're asking, but as best I can:
1. Yes, a cue is a conscious thought to do something, not an already embedded pattern that you have learned to do consistently correctly. The process of getting to the latter point often involves cueing, but once you're there, and doing it correctly as a matter of course without needing to specifically focus on it, that is no longer a cue.
2. I don't understand the Q. (pun intended)
3. Yes. Proprioceptive feedback is a tactile cue. Some people are inherently good at it while lifting and know where they are in space, feel the positions or muscular tensions that tell them about their positioning, etc... Other people aren't good at it but can learn those things via coaching and cueing.