This depends on your champion and Playstyle. While for most AP based characters his statement is true, it doesn't apply to all AD characters.
The main reason why Penetration stats are strong against Low-Resistance opponents is (as you have already mentioned in your question) because of the "True Damage". Obviously you won't really deal true damage to an enemy (or at least not often) but Armor or Magic penetration will increase your Damage output significantly if you are playing a spell based champion.
Most spell based champions do scale heavily with spell-level rather than with AP/AD. Obviously there are some exceptions to it but as long as you don't have a 0.8 scaling + on at least 2 spells spell levels are stronger than flat AP/AD.
Because of that buying flat penetration like found on Brutalizer or Haunting Guise is exceptionally effective for harrassment during early and even mid-game. It allows you to snowball and while flat Penetration isn't uber strong late-game it's still decent and certainly not wasted.
The biggest disadvantage to it is that lasthitting might get a lot harder since flat AD/AP is the stat to go with there. However if you are comfortable with your lasthitting skills you can safely go for Armor/Magic Penetration early for more aggression in lane.
Please Note that this is really only an advantage on Casters. Autoattack (Ashe/Jinx) or extremely high scaling characters (Zilean/Anivia) are usually stronger with more of their Flat damage stat.