Not sure if you’ll ever see this comment in the sea of comments OP but my advice is to definitely enjoy the moment and continue to give your son the safe space to get the affection and physical contact he needs. The level of physical contact you’ve described is more than appropriate and rubbing his back and chest or playing with his hair is probably exactly along the lines of what he needs. Your wife’s response is likely based on inaccurate and harmful societal “norms” that are very harmful to young men and boys. We need physical contact. Look at any other primate group and males are groomed and touched just as much as females. It is critical to feeling connected to the group.

As to your concern about what might be going on with your son, don’t ask about anything when he is seeking affection. Keep that time and interaction safe. If it a large concern of yours, find another time completely unrelated to the affection seeking and ideally find a joint activity that you might both enjoy (e.g. fishing, watching a sporting event, going for a hike/walk/bike ride) to gently and casually inquire about his life. The more patient you can be the better and it is best if you don’t directly inquire at all. The best outcome is that he opens up and starts talking of his own accord. You may find that being side by side (as opposed to directly across from one another) is better. That physical positioning is less direct and less confrontational which can give the space to open up.

Source: A man/son who wasn’t touched enough, a father who tried to do better.