As far as your issue goes, why not just fix all the query strings with a couple lines of mod_rewrite and not worry about where they came from?
Well, that wasn't really the point. The point was that g### can't distinguish between a parameter that is part of the page's own name, and a parameter that was appended by the linking page on someone else's site. Especially when the parameter in question is "newwindow" which should be near the top of the list of "Parameters that will always be ignored everywhere". </ot>
There's no way it can have the opposite effect if it's implemented correctly, because the pages should not ever be accessed, and if they are then you're simply noindexing duplicates of the canonical version. <snip> If they don't ignore the parameter for some reason, then both will be found and have the same effect as the "ignore" should.
... and that's exactly what I meant about conflating two different aspects of parameter handling.