I still have a rectal stump left. I originally thought that I was going to have a "barbie butt", but when I came out of surgery, my doctor informed me that he did not remove the stump. He said in his opinion it would have done more harm than good to me (I had surgeries on that area when I was a baby and have scar tissue).
I trusted his judgement and have had no issues with it being left intact.
However, I believe most of the time it is removed, I am just an exception. Always have been!