You're skipping over the step of calculating "effective skill". In roll-under systems, you add and subtract and add and subtract modifiers based on conditions. In a typical roll-over system, you have a base bonus, maybe a pre-calculated effective bonus, with environmental factors, against a "difficulty factor" which at worst the GM calculates on-the-fly based on circumstances. Mathematically, it's the same, but cognitively it's a little easier to add than subtract at the table ... and you can calculate many bonuses and difficulties ahead of time.
Originally Posted by Harwel
"On two occasions I have been asked [by members of Parliament], 'Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?' I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question."
- Charles Babbage (1791 - 1871)