I'm going to go ahead and agree with someone else who said it's just a symbolic thing that every master uses differently. In Eraqus' case he used the mark of mastery exam to demonstrate whether or not he had anything more to teach them. Aqua was the only master because she was the only one he thought was worthy of being called an equal to him.
In Yen Sid's case, I think he's just using the mark of mastery to see if Sora and Riku are strong enough to fight Xehanort. He basically just wants to find out if there's anything else they need to be taught before they're considered masters.