The diameter of the shaft makes up the difference for the thicker wall. So the only factor in penetration would be the larger diameter of the arrow. However in a well lubricated target like a live animal I don't think it would matter too much.
Dr. Ashby's results have showed better penetration with smaller diameter shafts.There has been some discussion that suggests all that is necessary is to have a broadhead ferrule that is larger than the shaft diameter - shaft meets little resistance with hole larger than shaft. He also demonstrates significantly better penetration with extreme FOC arrows. I'm not sure if he's said what shaft they are, but I'm willing to bet these are lighter weight carbons. I've tried building an aluminum with an FOC of 27-30% and adequate spine from a 70 lb bow, and have not been able to acheive it. Aluminum simply weights too much. I can't get enough weight on the tip. With carbons, I can easily get 350 grains on the tip of a relatively light weight shaft that is stiff enough to shoot it. These high FOC carbon arrows appear to out penetrate an equal weight aluminum quite easily, and I'm guessing that his statistics come from extreme FOC carbons. I do agree that this area of penetration hasn't been completely explored at this point.