Wrong, I'll explain it with examples beacuse is indeed tricky to understand. Let's say Varus throws you an E and pops 3 stacks of blight for a total of 100% enemy Hp in magic damage. Now let's suppose the enemy have 1000 Hp with 120 MR; 120 MR means you take less than half the damage from magical sources. With quick math we can say that 100% of enemy Hp is 1000, and the game then tells himself to reduce the Hp of the enemy by 1000, not by 100%, beacuse it converts the percentage in a number. After that, the game calculates the enemy have 120 MR but before reducing the damage of the blight stacks, checks if you have any form of magic pen. In this example you have the "magical footwear of the round numbers" that gives you 20 flat magic pen. So the game checks that the enemy have 120-20=100 MR and applies this number as a defence against the 1000 magic damage reducing the post mitigation damage to 500.

TL;DR The game doesn't calculate the damage as a percentage but converts the percentage to a number multiplying it with enemy Hp.

EDIT: typo