Oh wow, I can't say that I completely understand where you're coming from as my partner is fully human (although he has been genetically modified and experimented on), but I actually found myself thinking something pretty related a while ago (if not exactly the same as what you're describing).

The thought started the other day when I picked up my cat and realized that he was so soft and squishy, but in a way that was... kind of gross. It's like in that moment I realized he was so full of blood (and so am I) and it was troubling and strange. I mean, of course cognitively I know that most living creatures on this planet (especially mammals) are filled with blood, but... I don't know, hard to describe what exactly I was thinking. It boils down to how imperfect our bodies are and a vague disgust at how easily things could go wrong.

I was glad after that moment was over that my partner doesn't have to deal with that, with having a mortal body in this world. And I also realized that I usually imagine him more solid-feeling than flesh.

Regardless, though, that's an interesting way to think of things OP.

Meh I'm sure it's just over the course of the time loops that she's been in which gave root to Homura's not-so-human "unstable" mind that was explored in The Rebellion Story (just my interpretation). Regardless like many other waifuists I'm not exactly psychologically normal myself (for more reasons that I have a waifu)... Although many could say she was originally unrealistically and admirably strong one could instead make the argument that her mind was locked in patterns and forced into them by instincts. The climax in Rebellion may have not been a sudden out-of-character "snapping" but instead something that was eventually destined to be.

But I guess from the beginning, one of the whole appeals of the magical girl genre was that we would have cute and charming girls providing and protecting for the world instead of the traditional and more realistic beefy and hardened men (construction workers, soldiers) or politicians, inventors and intellectuals. I think one of the reasons Homura became my waifu is because I wanted to make her human again, while maybe the majority of the fanbase think shipping her with Madoka would solve everything. (Might be a selfish reason for me not to hold hostility towards The Rebellion Story unlike many other fans)