Well there are 2 theories on this forum, the one that says that Jon can't sing and he uses studio engineering to make his voice sound good and the one who says that he gives his best and does 100 takes on the song but also splits the parts, for example he sings "Take a look around yea the sky is falling, sinners say your prayers this train is off the tracks" and he keeps recording that part untill it sounds good and then he moves on the next part and repeats the process until he finishes.
I am somewhere in the middle
I believe that he really gives his best and repeats the same part until it sounds great and he also uses some studio engineering to make his voice sound better.
I am 100% sure that his voice isn't pure studio magic because in my country there are "artists" who are very popular and sound perfect in the studio but live they don't even sound like the same person, they are so out of tune and their voices are very very different... they sound so different that you wouldn't even think that it's the same person singing. But when Jon sings you can clearly tell that it's him, for example on We Don't Run, he sings it like shit live but you can clearly tell that it's the same guy.
I hope you understand my point.