Penetration should be unique. You should chose % OR flat, not both
I think it would be more healthy. Tell me why if you disagree.
Here is the idea: You want to do damage? You build DAMAGE You want to be tank? You build RESISTANCE You want to be strong against squishy? You build flat penetration You want to be strong against tank? You build % penetration
This should be the logic, which would create strategy, but it is currently not: in competitive and in non-competitive, you want to do damage? You can build all penetration item. wurf.
The point is: Assassin should be strong against squishy, weak against tank. Anti-tank should not be able to assassinate a squishy.
In order to do so, penetration should be a unique passive (hence you should be able to use this passive from an item only once), therefore you would have to chose between flat and % pen, if you want to be an assassin or an anti-tank (and if you want DPS, don't bother: just build damage).
You shouldn't be able to accumulate flat and % penetration stats:** it kills the logic of strategy behind the design**
Maybe, you could cumulate flat pen item passive OR cumulate anti-tank item passive, but not both.