I think it depends, personally. Some champions they have are specifically designed to bust through anyone - no exceptions. I honestly, really and truly, think it's fine on Vayne because she's outright designed to be this auto-attack-centric carry that sweeps through your whole team later in the game one at a time, and her entire kit revolves around this idea and enforces it.
The problem with flat amounts vs. % true damage is that % is equally effective against squishies and tanks alike, while flat amounts are objectively stronger against squishies - some of whom may not be able to really afford to build defense against it until far later in the game. Transforming any source of % hp true damage to flat would be an outright buff to tanks for no real reason. Imagine trying to bust through Malphite or Mundo as Vayne late in the game if you had no % hp to help you through them (especially given that Malphite already has tools to help considerably against Vayne), and she's the League's premier tank-buster, outright designed for the role, with strengths and weaknesses that go along with that role.
Unless this whole thread is meant to be a dig at Fiora, because in that case I agree that her % hp true damage feels kind of superfluous and unnecessary. Nothing in her kit that I can see, besides low base damages on things that actually have damage, outright says 'hey, we need a huge % damage steroid!' She seems like she'd operate just fine with flat damage, or percentages in physical damage (or magical damage if you wanted to give her split scaling to make her a little harder to itemize against but not impossible, plus she'd share a primary damage source with the mage so your magic resist wouldn't be wasted).