I have the same problem when wearing loose fitting jeans--and all my insulated winter jeans are loose fitting as I've lost a lot of weight since buying them. I solved it with compression boxers similar to those worn by many athletes. I got them at an athletic sports store.
The problem I suffered wasn't the result of getting pounded into the saddle so a more comfy saddle wouldn't have made any difference. My problem was the general jouncing and bouncing--exactly the same problem marathon runners and many other types of athletes suffer if they participate in sports that cause the body to bounce around alot.
As far as I know the only solution is to bind 'em up close to the body with close fitting clothing so they don't bounce around so much.
Does your guy ever go to the gym? Wear a swimming suit? If so, he wears something to prevent bouncing abuse to his manhood. He needs to wear something similar when riding.
"Don't just feed it! Ride it!" And the People said "AMEN!"