I believe a RIOTer said in response to someone else bringing up the claim that the flat magic pen and percent health burn don't belong together, that they actually do belong together:
he pointed out that flat pen is most powerful against a target for which the flat pen completely or nearly completely penetrates all the enemy resistance.
40 flat pen against a target with 45 magic resist is more of a hit to the target's durability than 40 flat pen against a target with 145 magic resist.
another way to look at it is each 1 magic resist forces the enemy to do 1% of your max health in additional pre-mitigation damage to kill you. So 40 magic resist when you have 1000 health allows you to take 400 more magic damage. Going from 100 magic resist to 140 magic resist allows you to take 400 more magic damage before dying, although because you had 100 magic resist and 1000 health already, you were already able to withstand 2000 magic damage. Going from 1000 to 1400 is a bigger percent jump than going from 2000 to 2400.
Hence, removing a flat amount of magic resist (or penetrating it) is much more devastating to a target that doesn't have a ton of magic resist in the first place. Thus, the liandry's combination of flat pen and percent health burn is specifically meant to punish tanks that have lots of health and armor but very little magic resist.