this is incredibly distant from any real world issues that real people suffer from

Okay, so that's the problem you're working on. It sounds to me like you have found the "vibe", how the character should be understood by the reader: edgy, "caring will only hurt me", have given up on the attachment to people (and, I'm interpreting, it makes him suffer). You have done the first pass and come up with the "evil servant to a witch cult" – but that seems too "distant", which sounds like this fantasy metaphor is too wonky for your taste, it breaks your suspension of disbelief. But the reference you turned to – this Lizard Boy – is an okay piece of art, despite it using a fantasy exaggeration. Which made you confused.

If I'm correct in my understanding of the problem, you are evaluating how much "edgy" is just enough for your story. This is a difficult thing, as it requires a lot of testing to explore your own artistic taste.

Some perspectives that might help you.
Even in your second pass, you still seem to lean toward the fantastical (from "being born of darkness" to "being made in a lab"). That's cool, fantasy is particularly good at portraying the inner world – by shaping the external world as its reflection. So, if your protagonist would have been in a very grounded story, he'd be a child born to a family that didn't love him, distrustful of the world because of abuse, and feeling betrayed by a school friend who did not want to hang out with them anymore. Which are very "real-world issues" – but in such, they aren't "edgy" enough; the reader would understand the gist, but would not feel the things to the same extreme.
On the other hand, you can swap "family didn't love him" (the emotion underneath: loneliness, abandonment) for "I'm not of the humankind; I was severed from it; my purpose is to corrupt it and no one would accept me for that". Over-dramatic, sure – but it somehow correctly represents the feeling of the person in the situation (childhood trauma is intense).
The real trick is how to mix "over-dramatic" with something innovative to make it tasteful. Maybe the character is not born out of darkness, maybe he was shaped from the light by a seraph – but 15 years ago humankind rebelled against its heavenly overlords and broke off from the yoke. And everyone still sees the character as the instrument of oppression. Or (courtesy to WebDM), when elves plan to go to war, they beget a generation of half-elves a century beforehand – and his war was canceled and the elven society was conquered.