When he says Base Damages he's means the damage of a skill without the scaling ratio, not auto attacking.
What he's asking is it better to build lots of Armor Pen because the base damage is high enough that Penetration scales better than actual AD, or is penetration deal less damage than AD stacking. Fiora is in that very close state of balance where Pentration and AD are very close in effectiveness, but that AD slightly outscales Penetration in a normal situation.
In my very limited Fiora Jungle experience (I've only tried once on live, and a couple times on PBE), I normally do:
->
-> 
and then depending if I need more damage or chase power I either build
or
first respectively.
After that, it really depends on how the game goes, but I'll normally pick up
as my last offensive item and then by that time the game will be over.
Flat penetration should be sufficient enough on Fiora until mid/late game, but if the enemy starts stacking armor, I'd pick up the LW before finishing Youmuu's.
EDIT: Fixed up the items.