So I made two end-game weapons, one is a sword, the other is an axe. Their stats are identical besides their strength and damage bonuses.
What I want to know is, how do these stats translate into practical damage, and which one should I go with?

So I made two end-game weapons, one is a sword, the other is an axe. Their stats are identical besides their strength and damage bonuses.
What I want to know is, how do these stats translate into practical damage, and which one should I go with?

personally I'd go with the Axe. The armor penetration comes in handy as it removes some of the damage mitigation enemy armor provides thereby increasing overall damage.
Each point of strength translates into 0.5% Attack, plus bonus damage against Guard. By now, you probably have effective means of taking down guard quickly, so you can just read the Sword as +50% Attack and the Axe as +48% Attack. Armor Penetration isn't the most effective offensive stat for 2H warriors, but 28% of it is likely to outperform 2% Attack unless you're dealing with an enemy with very little armor, so I'd go with the Axe.
That said, since you already have both weapons and they're both top end, I'd keep both around. Keep one as-is and use it as your dragon-slaying weapon, and swap out the rune in the other one to make it more general purpose or specialize it against different enemies.