I'm sure it does baste the meat. However, I haven't done an experiment to see how the two parts cook separately. Jim or Warren probably know better since they're more experienced cooks.
However, IMHO, there would be a few advantages to cooking the muscles separately: 1. The flat and the point cook differently and to be able to have both cooked perfectly at the same time, or close to the same time, has not happened when I've cooked a whole brisket; 2. There is a thick layer of fat between the muscles, and this is one UGLY piece of fat; it looks more like tripe than back fat and you shouldn't serve it with any competition level brisket - it's way to greasy, fatty and soft; and 3. You can trim off all ugly pieces of fat (see no. 2) prior to cooking so that youre presentation meats will look much better. I saw Adam Perry Lang of Daisy May's Barbecue on one barbecue competition tv program where he did exactly this.
I cooked a small brisket two weeks ago on my XL BGE and had the same issue. The flat portion of my brisket was slightly overcooked and my point/deckle was undercooked. Personally, I would never eat the flat if I had a choice. :muahaha: