You can't do true damage with anything that doesn't say true damage. You can do increased magic damage to squishies assuming they have no MR even in runes and you build every penetration item, but not true damage. It will just add a multiplier to your damage like it always does, but instead of a number below 1 to reduce it, the multiplier will be over 1 which increases it.
Taking this to extremes, a mage with every penetration item, mastery, and rune against a ranged champion with base MR:
30 pen from items, 19.5 from runes, 5.75 from masteries = 55.25
35% from void staff
38.5*.65-55.25 = -30 MR
2-100/(100+30) = 1.23 damage multiplier
Before penetration, it is 100/(100+38.5) = 0.72 damage multiplier