if what you're suggesting is true, then more important instructions like "Don't delete the production database" are a problem. I shouldn't need to consider how to phrase "Don't delete the production database" in a positive manner. Isn't the point of an AI agent that it understands my intent and I don't need to hold its hand? I'm not saying your suggestion is wrong, I just think that suggests a limit to what these tools should be used for if that's the case.
My guess though is that it probably ignores some of the positive instructions too, and the hardcore AI users mostly don't notice because they probably aren't reviewing the work.