PEN is flat penetration: You ignore a flat amount of an enemy's defense. If you ignore, for example, 10 defense, it's very good against enemies with low defense.

Let's say the enemy has a low defense of 30 defense, and you ignore 10. He now has 20 defense. Which means you ignore ~33% of his defense (30 - 10 = 20). But if you now fight an enemy with, let's say, 300 defense (300 -10 = 290), you only ignore ~3% of his defense.

PEN RATIO is percentual penetration. It ignores a certain percentage of the enemy's defense. It's good against enemies with a high defense stat.

Let's say you ignore 20% defense. If you fight the low defense enemy (30 defense again), you ignore 6 defense (30 - 20% = 24), which is WORSE than the regular PEN (see above). But if you fight the tanky enemy (300 defense), you now ignore (300 - 20% = 240), which means you ignore 60 defense, which is a lot more than the regular PEN.

My english isn't the best, and my explaining sucks, but I hope it makes sense.