With an adjustable comb and butt I assume that the comb has been lowered to the maximum with no spacers? If so I would check the POI for both barrels. Neil Winston has one of the best methods for checking POI IMO.
POI and pattern at 13 yards And:
More reading on his original methodology Having an adjustable comb and butt plate sounds like a trap gun, although this is a 20 ga. which is not a common trap gun. Double trap barrels are often regulated for the bottom bbl. to shoot high on the rising first target of doubles and the second to shoot flat for the second target.
In any event would certainly make sure that it is not the gun in addition to the shooter. I know of several people that have had to shave down their comb to get it to shoot flat, even with an adjustable comb. And it seems to be more common with newer guns in the last decade or so.
His mount as mentioned is important, it is certainly worth verifying his head position on his mount. Being young he may be crawling his head up toward the front of the stock. If LOP is too long which it often is for young shooters I usually see them mount with their head further back though.
If he is serious about shooting skeet there is a lot to be said for shooting high and floating the target. It was my preferred method for many years especially in strong winds. Hard to hit the target when you can't see it because your covering it and it is dancing. But I have gone back to flat shooting guns for all clay venues and hunting. I have 2 guns right now that I am considering selling because I can't get the POI down where I want it. At least not with more work\modifications & money than I want to put into them.