I would say qualities only ever count as one, even if they have multiple levels or ratings.
If you are taking Built Tough 4, you are not also taking Built Tough 1 through 3. In other words, you don't write BT1, BT2, BT3, and BT4 on your character sheet.
I see what you mean, but I think this approach falls apart with qualities like Allergy; how do you count the numerous available choices except as a simple Quality?