Yeah. What most people don't realize about the two is that LW items only bypass bonus armor. Any base resists stay at their full values. Basically, armor from runes, masteries, items, and abilities is reduced (to hurt tanks - ADCs are designed to be the designated tank-killers), but built-in armor is untouched. Since flat applies before percent and, IIRC, flat applies to bonus armor first, this also means that flat lethality is less useful. If you take off 10 armor with lethality, and you have Last Whisper, you would've already ignored 4 of that 10 armor you removed. It's not taking it out of bases - you're making a %change to a smaller number.
Magic pen has the same issue with redundancy to some extent, but Void Staff bypasses bonus and base MR. That means the overall pool you're reducing is larger, and the percentage of the pool that you're taking off with flat pen is relatively smaller while still being the same in terms of actual value. Now, the numbers on Void Staff are a little smaller from a pure percentage standpoint, so LW's upgrades (just going to call them both Last Whisper from now on for simplicity's sake) are in theory better vs. tanks that build lots of bonus armor, but Void Staff helps against everyone rather than just resist-builders.
As a metaphor, imagine you're dealing with Kled, and you magic/armor penetration is %max health damage. Void staff would be like fighting Kled normally. It counts the combined health bar - both of Skarl's and Kled's together - as Kled's maximum health, meaning it does much more damage thanks to the much higher maximum health. Meanwhile, Last Whisper doesn't care - it only scales off of Skarl's HP, and ignores Kled's altogether. That said, it's bigger numbers, so when Skarl builds a lot of health, Last Whisper is better - thus, ADCs kill tanks well. However, when Skarl doesn't build much health, or, worse, when it's just Kled alone and he never even has Skarl (aka vs squishies), it's pretty much useless. It does nothing against Kled himself. Void Staff, despite its smaller numbers, does take Kled's HP into account when figuring out how much %max health damage to do. Thus, mages kill squishies really well.