Nope, you are saying you could build the human body better yet you don’t have a clue on how to build a human body. Wind pipe in the wrong spot? Ok, where are you going to put it? And how do you know a relocation wouldn’t intefer with some other bodily function?
Atheists differ from scientists because atheists present their position as concrete conclusive proof. No, a perceived design flaw does not concretely disprove God. And even if the human body did not have your noted flaws, you would find some other way to criticize. WHy are bones allowed to break? Why can’t a decapitated head reattach? Why didn’t God give us 4 arms instead of two? It would be endless complaints with the insane judgements that atheists hurl in defiance to a living God.