A noble savage can't work in a setting where civilization and agriculture did more good for the overall morality of humans as they don't have to fight over resources anymore.
Yes because "civilization and agriculture" totally stopped humanity fighting over resources. Oh wait, they didn't. If these are what is preventing you having conflict between groups of humans I'd gently suggest that you're doing it wrong., resources are always finite and if you've created a setting where to all intents and purposes they aren't your worldbuilding is faulty.
Lizard people obviously won't make great villains, the Icon of Simp is too strong, etc...
Or rather it isn't obvious at all. You can make more or less any anthropomorphized creature a great villain.
So, I decided to offload the evil into a single character, a member of the major arcana Bondrewd Best Dad, the user of Death 13. His abilities allow him to infect up to 100 people with nanomachines. He, depending on how long the machines have been in the victim's body, can control a person's muscles and even blow them up. This ability is a gorier version of Hokuto Shin Ken with at-convenience remote activation and ranged attack added. However, that most likely won't be enough.
This sounds like reasonably "horrible" power for a villain to have - but it doesn't mean jack without a an actual villain to use it in villainous ways. It's not the power that makes the villain - it's how they go about using it, what their plans and goals are.
As you probably guessed, Best Dad is based-off of Bondrewd from Made in Abyss. That guy is hands-down the best villain ever. Despite being the epitome of evil and turning children into literal moe blobs to attain Scientific Triumph, he has been memed to pieces (spoilers) and was, you guessed it, nicknamed 'Best Dad' by the fans. Here's a short vid to catch you up on why Bondrewd is a monster.
I hadn't guessed, mostly because I'd never heard of Bondrewd. I had a look on a few "top x villain" lists for various mediums and no mention of him. So much for "hands-down the best villain ever", maybe "best villain no-one's heard of"?
I want to emulate his character, but I don't know why he became so popular, avoided becoming the next Umbridge, and attained meme status. How can I write a similarly engaging but clearly and irredeemably evil character?
So far you make it sound like you've done nothing but an off-brand imitation. So I don't know but maybe avoid doing that? Looking at an existing character and saying you want to emulate them - particularly in the way they affected readers is fine in of itself, but if you're starting out from a place of not understanding even the basics of why you want to emulate them, if you're just saying "wow this character is really popular, I'll take one of them please" then I'd suggest you're looking at this from the wrong direction and you're dooming yourself to fail.
Since I'd not heard of this guy I did a quick google and from what I could glean from the villains wikia entry it's not hard to understand why the character would be seen as a particularly "evil" villain, they seem to be the familiar trope of the evil mad-scientist who conducts horrible experiments on children and anthropologically speaking most people are going to agree that doing nasty things to children is worse than doing nasty things to adults. Especially where the role would traditionally be a caregiver (or at least caregiver-adjacent). Adult readers/viewers don't want that to happen to their children and kids don't want it to happen to them. Horror for all the family!
At first glance there doesn't appear to be anything particularly special or unique about them, perhaps there's something deeper that requires one to be a fan of the manga to understand but I can't say I have any inclination to find out.
And I have to say that if you're going off the amount a character get's memed about as being some kind of barometer for a character being successful I'd exercise caution. Because along with being cringeworthy forgettable drek 99 point whatever percent of memes have very little to do with the source material beyond a shared familiarity with the character and a perceived humorous play on the character and something else, in short no serious content creators are out there writing stuff going "how to we make this meme-able?", they don't drive the popularity of something because they are either intended as stand-alone jokes that you can "get" without know the source material or they're in-jokes between fans of the material. There can be a correlation between a well-done character and them being a meme-subject but that doesn't mean there's a causation.
Irredeemably evil and engaging characters are certainly do-able - but as I alluded to above the roots of this lie not so much in what powers they do or don't have and more in what they do with those powers and their motivations. So start there, what dastardly objective is this villain trying to achieve and why are they trying to do it. Check out "Evil plans - how do you come up with interesting ones?" for some guidance on how to go about this. If you want to seek inspiration from existing villains then seek out what made them great villains, how did they make the reader feel? Why were they a particular challenge for the protagonists? What character development did they have? What character development did they drive in others? Not "did some weebs make memes about them?"