First series has her talking with her scythe, the next one has her preferring torture, while MC tries to keep them in check in both: Ankoku Kishi Monogatari Tsuki ga Michibiku Isekai Douchuu I read WN for this a long time ago, so I'm not sure about this one: The Forsaken Hero
The "yandere" in Yandere Kanojo refers to yankee, not the usual yanderu (ill). The mc is a yankee, not a yandere. I remember the mc was somewhat receptive to his girlfriend in https://www.novelupdates.com/series/these-dangerous-girls-placed-me-into-jeopardy/ . https://www.novelupdates.com/series/shinanai-otoko-ni-koishita-shoujo/ was a bit similar. But I think https://www.novelupdates.com/series...gled-by-my-female-junior-and-a-voice-actress/ may be closest to what you want. They didn't leave too strong an impression on me to be honest, but you may like them.
Found a one-shot similar to part of that the other day. Short. Has a female MC. https://www.novelupdates.com/series...rain-the-main-capture-target-to-be-a-yandere/
Koharu no Hibi. it satisfy most of your criteria He knows she is a yandere, he accepted. He prevented bad ending with his childhood friend although in the future .... let say yandere is heriditary so in future generation some bad ending that might happen is due to his decision to have children with her.
My House of Horrors has a yandere ghost attached to the MC's shadow. MC uses her like a nuke because she is a very powerful ghost Spoiler: Q novel Fair warning its a Q novel but PM if you want a link to the none Q
Tsuki felt like it got watered down after the Limia's second rescue till when the puppet revolt started. Ankoku is pretty good. The misunderstandings are funny and it should go the harem route, but idk how it ends up. At least till end of vol 5 it was him mostly trying to keep low-key and hold back the yandere, apart from Spoiler that time with Rena. It was enjoyable, especially seeing that he's supposed to be the villain against the summoned hero which is rare.