I use this at times that don’t even indicate a conflict or an initial gut response. Sometimes the “yes” is merely an acknowledgment of understanding the other person’s question.
Example—
Person: Are you gonna be leaving work at 5 today?
Me: Yeah, no, I’ve got a ton of shit to do and am gonna be stuck working late.
I knew off the bat that I wouldn’t be leaving work at 5, and I wasn’t conflicted. The “yeah” was an acknowledgment of the fact that this was a legitimate question and that I would understand why this person would wonder whether I was going to be leaving work at 5 today. Perhaps they’re aware of all the work I have on my plate, for instance. So the “yeah” expresses this idea.
Is this the kind of “yes—no” to which you were referring?