Yep. A rifle has to be zero'd for the shooter. Some folks might find that they can switch rifles with a buddy and be very close, some folks find that they switch rifles with a buddy and they're way off. A rifle zero is dependent on lots more than the alignment of scope and barrel. It will shift depending on the shooter, on cheek weld, on how the rifle is handled, whether it's fired off bags or off a hard rest, whether you use a sling, the list goes on and on. Most of my rifles fire differently off the bench than they do from common hunting positions. With sporter rifles, there is also a difference between cold barrel and hot barrel.
Yeah, what you describe is pretty common. Let your son zero the rifle for himself.