And it's not like it's always a sacrifice. When players are 18 or 19, playing them 48 mins out of position in a league game tends to mean a defeat. But you can use it to save enthusiasm and manage the other games better. However, when they become older and less of a liability, playing them out of position can also mean a world of mismatches for your opponents (just look at some of the games of the Czech NT!).
So I have to agree that this current training format is one of the best features of this game, and doesn't need any major changes.