Sounds like he has an underbite...the lower jaw does have hopes to grow when they are puppies to have an even bite. He still has a bit of time, but I would think it would've happened by now. If he has no problems with eating then it is just cosmetic. Usually baldness would be at the injection site for shots...so I dont have any idea for the top of the head unless he had his hair up and he rubbed it out? I would have it checked out for sure
Congrats on your new baby!!