Having "special interactions" among different options seems like a bad idea. If you actually have specific cases where the kinds of logic you describe seem necessary, there's probably a way to simplify the interface. If you're just imagining that such situations might arise, don't waste your time worrying about it, because if they do, there should be a way to simplify things.
You write user manuals for these tools, right? If an accurate description of how the options work is too complicated, users are going to use it the wrong way and get results they don't want.