The key consideration is the temperature of the surface of the meat getting dripped on, or basted if you will. Even though you would have a brisket or pork shoulder on the smoker for 8, 10, 12 hours or so... the surface of whole muscles meats would be the same as the pit temp in a pretty short period of time, so surface baddies that were present when the meat went on are killed, and any baddies in any drippings would be killed in pretty short time. Look at some of the big commercial smokers with the revolving trays.... they are designed so drippings fall from one tray to a lower tray. I personally don't put chicken above other meats, but from a food safety point of view even chicken drippings are safe if they get on other foods while everything is in the smoker.This is just my two cents, but I would think you would want the beef on top. Undercooked pork presents (in my mind) greater potential health risk than undercooked beef. So if you pull the beef first, the pork will continue to cook it off. If you pull the pork first, any drippings from the beef shouldn't present an issue.
The key consideration is the temperature of the surface of the meat getting dripped on, or basted if you will. Even though you would have a brisket or butt on the smoker for 8, 10, 12 hours or so... the surface of whole muscles meats would be the same as the pit temp in a pretty short period of time, so surface baddies that were present when the meat went on are killed, and any baddies in any drippings would be killed in pretty short time. Look at some of the big commercial smokers with the revolving trays.... they are designed so drippings fall from one tray to a lower tray. I personally don't put chicken above other meats, but from a food safety point of view even chicken drippings are safe if they get on other foods while everything is in the smoker.