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Hello :3
Great question! I can totally see where you're coming from and why it would feel out of character, so let me explain my thought process for that specific scene:
It starts with them talking, and Leshi specifically asks the MC if they "understand the price of being with (Nyxia)". What Leshi is trying to do here is to call Nyxia out on his behavior to make him lash out at either the MC (most obvious way to get rid of them, because that's what Leshi wants: to get rid of you so that Nyxia will stay with him) or himself, so that he can guilt trip Nyxia later like he does in the scene leading up to either the good or bad ending. The logic here is not obvious: Leshi knows that Nyxia knows that he (Leshi) is trying to manipulate him (Nyxia), so he's  trying to perpetuate Nyxia's toxic behavior through challenging him on it so that he doubles down (as Nyxia doesn't want to do as Leshi says, even if he ends up doing just that in the end) and ends up killing the MC from neglect later on (what happens in the bad ending). When they are talking, Leshi keeps calling Nyxia out: the line that get's cut off by Nyxia would have been "It is that, for your whole life, you will be swindled by him (regarding the "price" of staying with Nyxia)". He later states that Nyxia is "scared of being sincere" and, when Nyxia tries to sympathize with the MC by saying it's a fair wish to have (and do just what you described, try and talk it out with them), Leshi immediately cuts him off by saying that "Nyxia is acting on impulse" and "will say anything to get on this human's good side". He is doing this to get under Nyxia's skin. Nyxia retorts by saying "You will not throw me off with this haphazard ramble", referencing the fact that he knows Leshi is trying to manipulate him, to which Leshi replies that he (Nyxia) is just trying to justify his behavior by putting the blame on him (Leshi), as he always does. Leshi then leaves, giving Nyxia no room to explain himself.

The reason Nyxia kills you is because Leshi's bs worked: Nyxia is pissed off at Leshi for calling him out, but he can't deny his words in his mind. Nyxia is conflicted because he is only doing that to the MC (drugging them so they can't leave) because he has severe abandonment issues that Leshi encourages (he tries to make Nyxia kill every human he comes across in one way or another), and Nyxia knows this behavior is unjustifiable. He is torn because he does genuinely feel bad for all of this, thus his insane mental gymnastics throughout the rest of the game. When Leshi calls him out not only on this but also on blaming him (Leshi) for everything he does wrong, Nyxia feels hopeless, because he knows it's true but can't seem to stop (the reason he can't stop doing all of this to the humans is because he fears they will leave him and so must keep them there by all means necessary, and Leshi is allowing all of this to happen precisely to have Nyxia on this position in which he is depressed that he has no companions [because he killed all of them] so that he can be the one that get's to be there for Nyxia. Nyxia won't cut leshi off because he likes Leshi). 

And so,  since he can't bring himself to blame Leshi and he has to deal with the MC anyway, he lashes out at them instead. He tries to find a reason for it, that's why he ends up saying "I thought you had some sense left within you", as he is now trying to shift the blame on the MC 'not comprehending' their "deal" (that they are meant to put up with anything Nyxia does to them). Nyxia's throught process is that, because the MC spoke up that must mean they don't want to be with him, and because Leshi has 'tilled the ground' so to speak, Nyxia momentarily feels like there is nothing he can do to change the situation. He can't let you leave, because you'd get killed anyway, and he doesn't want to keep you around right now because it would remind him of all that Leshi has said and all that he's done in the past, so he ends up killing you instead.

I agree with you that it's irrational, but it's meant to be. This sequence is meant to show how deep into Nyxia's mind Leshi is, but I can see how that wouldn't be quite clear! I suppose I could work on improving it at some later time, but for now I hope you got the gist of what's going on in that scene (or at least what I tried to write) :3 

I hope this all made sense (?) I am. quite eepy. Feel free to inquire more lol