The only difference, as you said, is if you want to sell the whole stack, or if you want people to pick their desired amount individually.
In both cases you set the price per unit, yes. But I would say that most people, while comparing item prices, check the price of a single item. Basically the game does the math for you if you want to sell a stack instead of single items.
Edited, Oct 2nd 2010 9:48am by FanciatheDragonkeeper
FFXI: Rynaria - Mithra on Kujata [retired]
FFXIV: Fancia Dragonkeeper - Miqo'te on Besaid