So the players just "figure it out" when the situation comes up? That seems confusing. Plus, what happens when you have a full yard and Charmbreaker Devils in play? How on earth is that game not going to go to time if one player insists on recording, shuffling, and reordering the graveyard every upkeep? Could you be sanctioned for slow play based on your choice of how to deal with the random graveyard effect?
If you are making a conscious decision to use a needlessly slow method of resolving game mechanic, I can't imagine any reason why you shouldn't get an infraction.
I really don't see why you're making such a big deal out of this. It's the exact same things as if an opponent was being unreasonable about any other aspect of the game typically left to personal preference. You call a judge to make them stop being an idiot.