First of all, the difference between 78 and 79 mph is negligible. What you may be seeing is nothing more than the error range of the gun you're using, or something more related to the typical peak and fall of a pitcher who gains speed as he limbers up and then starts tapering off as he fatigues.
Secondly, the difference in velocity typical between the 2- and 4-seam fastballs is not a matter of whether you have seams under your fingers in the grip, but rather, of the fact that a 2-seamer typically encounters more "drag" in flight. The same thing that enhances the movement reduces linear velocity a tad.
If the pitcher is under the impression that the thing that creates velocity is his grip on the seams -- a misconception -- then the problem may well be that he is squeezing the ball a bit more tightly on his 4-seamer. This can also happen when, from lack of experience/comfort with that grip, he just grips it tighter out of nervousness for his ability to control the pitch. Grip tension can lead to greater tension all the way up the arm, too, and all that tension robs velocity.
Encourage him to take his grip, then relax and let the ball whip out of his hand without forcing it.
As for the comment that the differences between the two pitches are overrated, hmmmm, how should I put this? Maybe you're not doing it right.
Ever watched Greg Maddux pitch? You don't get his kind of movement with a 4-seamer, esp. once you leave the youth league, raised seam baseball behind and move into higher level ball where the seams are flatter.
True, you can do things with your arm action to accentuate movement using either grip, and you can refrain from changes to arm action as well. But if you throw your 2-seamer and your 4-seamer exactly the same way, most commonly you will lose 1-2 mph on the 2-seamer, and most commonly you will gain sinking and/or tailing action.