Beware: I write code, not fiction.
Very hard question. I have tried may tools for note taking and brainstorming, and never found the right one for me. It's a very personal thing. Each one of us organizes his ideas in an specific way, and finding a tool that fits that way is nearly impossible (unless you make it).
I would be tempted to recommend some very configurable tool, but personally I find that tends to make me spend more time configuring than doing, because I am a perfectionist and, even worse, I tend to adapt my way of thinking to the project at hand.
There is people that tends to conceptualize things like a tree, where each idea hangs of another one. There is people does it like a cloud, where any idea can be connected to any idea, with not much structure.
There are many writer tools (free and non-free) around, I imagine you have tried many of them and know them better than me.
I found myself tending to create tree-like structures, and found that usually tree based tools tend to be too busy for me, and I tend to lose my focus with them, so I ended using the folding features of a text editor to create my notes, creating subsections using tabs, and hiding or showing things using folding, so when I think about something I can see all the relevant items at a glance with no effort. I simply hide with a click what I don't need. And making radical changes is usually as easy as cutting and pasting, and use the tab key as needed.
Probably not your cup of tea, but I don't really know how your process work.
For example, answering questions back an forth sounds like the perfect work for a chatbot; but, since you don't want LLMs, I assume I'm not getting your meaning.