Although most of the time in Sandbox RPG's I am bothered by it, I am glad there's a warning at this point.
Although I have to agree it takes power away from the ending if able to play after the ending, I do love to role-play the fact that the present danger is solved, and now it is time for me to find a place in the wasteland. Be it as a wanderer or just settle down and life my life out quietly.
Another thing is that I love my character and would hate to part with it after our epic journey.
In most games it is possible to replay with the same character, which eases the pain a little.
So yeah, I'm bothered with it, but frankly I do not care about it that much.