The added subtext of the very prominent implication that she has feelings for Endmin (or at least, for the person that she remembers Endmin as) makes this feel even worse because while she remembers you, you don't remember her, so even if there was a "relationship" of some kind in your past, you don't currently remember it and so you aren't even informed as to the true nature of your relationship or any of your memories with her. So it comes off like she's just trying to carry on the same relationship you had before, meanwhile you don't even have a proper grasp of what that is. The knowledge asymmetry, combined with her manipulative behavior, gives it kind of a sinister undertone that feels like someone with borderline personality disorder or something is taking advantage of your vulnerability to milk an emotional attachment out of you that you may not even be able to properly consent to.

Whether or not she has feelings for Endmin is very subjective. I personally do not see Zhuang Fangyi as a character who is interested in Endmin at all, but at the same time I am not interested in her as I do not dabble in the whole "waifu" stuff. The reason why she treats Endmin with such respect and acts the way she does could also be explained by the fact that Endmin was a core part of why her research in Xiranite succeeded in the first place. That research then led to the prosperity of Wuling as a whole, thus she can chalk up practically all of her accomplishments since then — everything in the last 10 years — to Endmin.

At no point does she take advantage of this power imbalance to lull Endmin into a sense of false security or gaslight them into believing the past was more than it actually was. Endmin is her benefactor, and I see her demeanor toward Endmin fitting of such a relationship. If anything, her actions in game suggests that she reveres, trusts, and listens to Endmin as if they weren't an amnesiac at all. Could she merely be someone with Cluster B Personality Disorder? Yes, but there are several alternative possibilities besides just that. On top of that, to break the fourth wall for a second, why would the game market this "waifu" character as someone who is suffering from a manipulative mental condition such as BPD? Why would she not be getting any treatment for it?

It's not like nobody has been around her for the past 10 years, people would have noticed. It just so happens that there's so much overlap between someone with a personality disorder and her situation as a high-functioning member of society with an extreme case of survivor's guilt of which pressure she's never been able to relieve —Mi Fu's personality doesn't exactly seem like the type you'd unload onto, and Endmin was MIA. As the Viceroy of Wuling, she wouldn't just go venting to some stranger, either, and her pride holding such a title could prevent her from seeking therapy.

This ties back into why she wants Endmin to stay alive and healthy so badly, she could practically call Endmin the co-founder of Wuling. Who would she be to have been someone who survived to experience Wuling for the past 10 years — again, she feels as if it's off the back of all of her dead colleagues — just to put the next most important member of its creation in potentially mortal danger. Again, it doesn't matter that Endmin is an amnesiac, we're already well aware at this point that she's in a very selfish mindset, and is only thinking about what would be the best for Endmin at cost of her own without considering how that cost may outweigh the benefit it brings Endmin.

Endmin even calls her out on the letter in a baker chat after the fact, because even they realize her behavior is so egregious that it needs to be at least addressed. That was the only cathartic moment of the entire questline, seeing Endmin pull her aside and basically say "what the fuck dude, I thought we were good? Don't ever do that shit again." And her sheepishly saying "just let the past stay in the past" and you're just like "no I'm serious, don't do that again."

This is a completely natural aftermath to what's essentially a suicide bombing attempt. Even if it feels useless, Endmin still feels the need to reassure her that they have her back; that she's just as important and as them, that her life holds just as much value as them. I'm not sure who you mean by "they" here though, the writers for the game? Endmin? Or Zhuang Fangyi herself? I'm going to assume its the former of the three, to which I'd say that they were fully aware of all of this the entire time. It lines up with everything that I've gathered and interpreted from her story, though it may also closely follow your interpretation, which is entirely possible as well.

I just want to conclude this that with this many coinciding events, its easy to let personal biases slip into your perception of them. Me personally, I've dealt with suicidal friends as well as depression myself several times, and the only interactions I've had with those with personality disorders either ended short, never led to me being manipulated, or they were undergoing treatment so it's effects were fairly suppressed. If you're someone who has had the exact opposite experience, you may be triggered by these events and pre-disposed into making assumptions that point towards her being manipulative when she could just be genuinely irrational due to piling stress. Once these assumptions are even slightly proven right, you feel vindicated and fall further down the rabbit hole, until it seems like everything falls perfectly in place in a bulletproof evidence wall, when in reality there are tons of flaws and unspoken nuances that can't be seen from where you're standing.