Armor pen went to lethality because of armor per level, right?

Snowballing was an issue BECAUSE of armor per level. It meant 15 armor pen was worth more the earlier in the game you bought it. The intention was to smooth that out by making it scale with the enemy level. The same problem can come into play to a lesser extent if an AP champion snowballs and gets sorc shoes or Haunting Guise earlier than normal.

Except by that logic assassins would be better at their job then mages.

Then why does literally every AD assassin item have lethality or armor shred?

I don't think you understand what I'm asking. I'm asking why flat magic pen doesn't function like lethality now that every champion has MR per level.