I believe that this refers to the lower lift arms, not the top link. Yes my tractor has multiple holes in the "pulling up" rods. I gain about 4 inches of additional height lift height at the end of the lift arms and a lot more at the end of the implement. I pretty much leave mine in the highest setting because the 3pt will go low enough with most all of my equipment. I have two implements that I could not lift high enough with the "factory" settings.
Some tractors have holes in the lift arms themselves at different spacing along the arm. Moving the "pulling up" rods closer to the tractor gives more range both up and down but at the cost of a lower lift capacity.
Shortening the toplink will allow the implement to lift higher but it also changes the angle of the blade in the ground. Yes, moving the top link to the lowest hole (at the tractor end) will also give more lift but the blade can be set more where you like it. Someone once said to me, simple geometry..