I've fished the Madison for over 20 years and have NEVER used a 6 weight. My go-to fly rod is a 10 ft 5wt GLX. If you are going to use large streamers, then take a 6/7 weight but for nymphing and for dries, even during the salmon fly hatch, I use a 5 wt.

I go with a friend and he takes a 5 and a 4 wt. I take a 10 ft 5 wt, a 9 ft 5 wt and a 9 ft 4 wt.

By the "confluence" of the Madison, are you referring to Madison Junction in Yellowstone Park where the Firehole and Gibbon Rivers join to form the Madison River? The Madison is a smaller river at Madison Junction than it is outside the park at $3 Bridge, for example. It is also a slower flowing river at the confluence of the Gibbon and Firehole; and during fall, the flows will be lower. For these reasons, I think a 9 ft 5 wt will be sufficient.

If you have a 6 wt take it as a "backup" but I would not buy a 6 wt just for this trip.