Put a beer butt chicken in the smoker today for four hours, with the 'sittin chicken' full of hard apple cider. Again, the results were delicious, but there was a subtle 'sweet and sour' taste to the chicken apparently from the cider (and the left over cider had a definite vinegary smell to it that it didn't have going in).
So what you put up the chicken's butt can affect the flavor of the finished product, however the affect is pretty subtle.