I tried the fat side down theory a couple episodes ago. IMO - the theory above make sense but I think it depends on a lot of factors, such as type of cooker, how close you are to the heat source, your cooking temps, etc. If you are cooking under 230-235 degrees as the article suggests, you will not 'boil' the fat out of the meat as it also suggests. Another factor - how much cooking temperature differential are you going to experience between the grate (bottom of the meat) and the top of the meat - we're talking like 3-3.5 inches max between them for a brisket. Anyway - given the lower cooking temperature and the other points I raise I don't think you will overly 'cook' the top or the bottom of the meat. I think it's best to cook with the cap up to render whatever fat you can into the meat (recognizing that most 'rolls off' anyway).