Joel's head naturally usually sticks out a bit whenever he's behind cover, just like his gun will sometimes point out past the wall when taking cover. It's a natural thing when game characters take cover. I have yet to ever see a video game that isn't forgiving to characters taking cover and pieces of their body slightly sticking out. Why? Because if they weren't forgiving, the game wouldn't be fun to play. You wouldn't be able to get close to the edges of any object or wall in the game because the limbs and hats and shoes and guns of characters would immediately alert the line of sight of any enemies.
Context. I've choked out people nearby and been caught, it depends on if you're in the line of sight and, after all, you have no idea how loud the choking is to that person, you can only hear it from Joel's magnified distance/perspective.
Ultimately, considerations are made for the gameplay and fun. That's why they have that dull bass noise get louder when your risk of being noticed is increasing.
In real life, if you were seen, you'd be seen, but in this game you can be in the line of sight for a limited amount of time before the enemy is actually alert to your presence. This varies based on context, like how close you are, the noise you're making, etc. But it's this way because this is how Naughty Dog found the gameplay to mesh with the type of stealth they were designing and it's how they found it to be fun, and I agree.
I'll give you this, but once again, the game just wouldn't be fun if it was overly harsh on you.
Real life stealth is not fun. It's boring, painstaking, takes forever, and you mess up once, you're done. It's not that the AI is dumb by mistake or anything, it's that Naughty Dog took considerations for the game to be enjoyable.
I don't care about you renting a game, but a Naughty Dog game being shit? Haha.