Armor and MR can be thought of as % effective health. 100 MR will cut magic damage in half and 200 will reduce it to a third.
Thus giving you 200 and 300% effective health against magic damage.
Most magic damage however comes in the form of burst. Doing a lot of damage quickly, but not so much over time. It's important to note A good chunk of AP Burst Can be mitigated, though Item utility rather than just strait up stats. Items like Zonya's and Banshee's veil. Their also tend to be fewer magic threats than Physical ones. (like towers)
And that's part of the reason why their isn't huge amounts of MR stacking. They don't need it. It's only really lame against certain AP DPS champs like Rumble, Vlad and Cass.