Here's the simple math:
Enemy armor is 100. They take 50% less damage.
Your attacks do 100 damage per swing/nuke, your marks give you +22% crit damage
You do 50 damage normally, and you crit for 111 damage due to the armor. The crit damage turns out to be an extra 11%.
With armor pen runes, you get 18 armor pen.
The enemy armor would instead be 82, and they would take 45% reduced damage
Your attacks now do 55 damage instead of 50, and you crit for 110 damage. You're not only getting similar benefits from the crit damage, but you're also doing more damage without critting.
29 armor pen with both Marks and Quints vs. 37% crit damage from Marks and Quints
Enemy has 100 armor
You do 100 damage with each swing/nuke
With Crit damage, you are doing 50 damage normally and 118.5 on crit
With armor pen, you are doing 71 damage normally and 142 damage on crit.
Armor pen marks are the better buy for almost any character.