Vayne's Silver Bolts are her way of hyper-carrying. Hyper-carries typically utilize some combination of %HP damage and/or AS steroids to chew through any target regardless of their resistances. Vayne has no AS steroid (on a champion whose entire damage output is auto attacks with no way to extend her AA range), so she has one of the strongest %HP damage effects to compensate.
Fiora has %HP true damage for thematic reasons. She's supposed to be able to out-duel anyone 1v1 by playing well and hitting the vitals. The whole idea of a vital point is striking through her target's defenses. It's either %HP true damage or a large amount of (bonus) armor penetration, and at that point the true damage is honestly simpler to grasp.
As for Conqueror, it's good in concept but the execution needs adjusting.
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Reduce the true damage conversion to 10%, but it scales up to 20% based on how much higher the target's Max Health is than yours. It's supposed to be specifically aimed at fighting beefier targets, after all, and the effect makes more sense here than on Cut Down (you know, that rune in Precision that I'm pretty sure literally nobody uses).
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Make the conversion adaptive, meaning only your dominant damage type benefits from it. Hybrid damage is already pretty anti-defense as it is, Conqueror doesn't have to double down on it. This is mostly a Jax nerf, though it does hit Irelia too since she has P/E/R for magic damage.