From my experience it most definitely is not "true" damage. My best guess is it's the amount of resistance it ignores. We can't really be 100% certain about this as it's description is simply "Affects Ninj/Tai damage".

Well... after some OP game, which basically copied this game without the combo system.
Which got same stats pretty much, how the Pen. worked there is > 100 of the stat where 1% dmg increase.

So let say you have 100 on Taijutsu Pen. then you increase your Taijutsu dmg by 1%.
btw this increase won't show in the detail of the character, only in battle you gonna notice it.
But atm is really hard to get Pen., Group Talents is like nothing.

But later on chakra system, I think Gold Pen. chakra, was like 450 stats each lvl.