The magic pen on it isn't really that helpful as compare to it's Armor pen item.
and 
only effect bonus armor, which makes them completely useless vs. the 20~75 base armor all champions get from leveling.
35% total magic penetration works vs. all Magic Resistance regardless of the source: and every champion starts with 30 base, melee's tend to get 52.25 at level 18.
For 45% vs. bonus gets better than 35% total:
With 25, 50, 75, and 90 base armor you need to strike foes with 123, 225, 338, and 405 bonus armor, respectively.
Or foes with 98, 175, 263, 315 bonus armor on those bases.
Another way of saying that:
is better than .
Outside of a Malphite or Rammus that are doing so well they're solo-carrying the game, you're just not going to run into the armor levels necessary for 45% bonus to exceed 35% total.
That said: the +15% bonus physical damage vs. opponents with +500 Max HP on Lord Dominik's Regards allow it to stay even with 35% vs. 0, 38, 95, and 130 total armor from 25, 50, 75, and 90 base: or +0, +0, +20, +40.
So Dominik's is actually good at shredding anything with more than 500 HP than you, but only tanky targets are going to have +500 HP on you for Dominik's to exceed what Void Staff offers: and generally speaking, only ~1/3rd of your opponents are going to invest in an HP heavy itemization direction.
Which still means is better 2/3rds of the time.
Since most mages do not have sustained damage (since most damage is tied to spells with CD) the % magic pen isn't really utilized as much as its counterpart
Magic penetration being useful has nothing to do with sustained damage.
Increasing the damage potential of a QWER burst by ~30% is increasing the damage potential of a QWER burst by ~30% at the end of the day.
At a certain point, backing your magic damage with magic penetrations is more cost-efficient vs. everyone than investing in more AP for dealing magic damage to all opponents regardless of what they did or did not build.
Everyone has 30 MR from bases, most melee's get 52.25 @level 18 from bases, and with MR scaling runes being fairly fashionable along with items like 
being things that will aid squishies in bolstering their MR as a game progresses: there's pretty much always going to be enough MR for Void Staff to work with when late game comes around.
This makes a really reliable 3rd major item on pretty much every AP carry.
Same can't be said for , which offers nothing but 40 AD vs. ~2/3rds of your opponents, a 
1300 gold value of stats for 2700 gold.
The magic pen on it isn't really that helpful as compare to it's Armor pen item.
The magic penetration on Void Staff is more useful than any armor penetration a single armor penetration item can offer at the moment.
