Imperfection. This is why each, and every situation you've just listed has been vacant of caution. Kishimoto himself is a human, and human's are insufficient beings in the manor of rationality in most cases, but what do we as debaters do? We perfect the imperfections. Yes, Itachi did not activate Susano'o/Yata Mirror until Kirin was fully acknowledged, and yes Madara did not erect an seemingly impregnable defense of Goudama. The reason is as I previously stated: "Imperfection". Humor me once again Waltz:
X: What if Itachi had used caution, concealing himself in Susano'o before the initial Kirin assault. Would the outcome have become any different? Honestly, I can't say it would've.
Y: What if Madara though arrogant as can be, had indulged in caution, fortifying his defenses with Guodama. Would the outcome have become any different? I believe so.
In every situation, if caution is applied the odds of survival increase, no matter what the situation. But once again, why is caution never implied canonically? Because Kishimoto isn't perfect. He doesn't assess the entire situation, he doesn't review every minuscule aspect which could change an outcome. We as debaters are arguably more intelligent in the aspect of perfecting his work, because we take these things into conclusion. This is why Itachi, nor Madara applied your scenarios: Because Kishimoto's lack of thoroughness.
My Analogy does apply, if caution is exerted. A man of caution, is a man who does not devalue, or overvalue another. A rock could symbolize the same lethality as a grenade to that of a man of caution. Logical deduction has many forms: Observing the content thoroughly, then reacting or Reacting to the situation off of an inference. They are both the same, yet alternate in initial maneuvers. So once again, you're wrong on intelligence vs instinct.
In regards to the scan you've kindly linked me, it's shown that Jinton can only pass through objects the user can see the other side too. If that isn't the case please enlighten me. I won't address the other context (Ohnoki hitting Manda in the teeth etc.) because I'm merely arguing Manda can evade Jinton.
Edit: Going out for a run. So don't think I've raised the white flag.