To add to this: the %damage increase you get changes pretty dramatically based on how much armor you're penetrating.
30 armor penetration vs. 30 armor causes you to deal true damage, or treat a target that took 76.923% damage as one that takes 100% damage from physical sources. That increase works out to exactly 30% more damage.
30 armor penetration vs. 300 armor causes you to treat a 25% damage from physical champion as ~27% damage from physical, which is ultimatly only a DPS increase of ~8%.
Worth noting base armor is ~20 @level 1 for most champions and even Sona exceeds 75 @18, so flat penetrations are always going to have enough armor to work with.
Alternatively: 30% armor penetration vs. 30 armor is only ignoring 9 armor, or treating that 76.923% damage from physical target as a 82.645% damage from physical target (a DPS increase of ~7%).
30% armor penetration vs. 300 armor treats a 300 armor foe as a 210 armor foe though, or 25% damage from physical to 32.258% damage from physical: an increase in DPS of ~29%.
So %penetrations are a counter to armor, armor counters flat penetrations.
Those stats dynamically change the gold-to-power value of one-another (where 10% more DPS from AD/AS/AP is always going to mean 10% more DPS regardless of how much armor/health/%AS slows/MR your opponent does or does not have).