Batting out of Order (w/ balk) [OBR]

[David Emerling]

I read the following from the following umpire's blog:
https://umpiresblog.wordpress.com/ (you have to scroll down a bit)

"...a balk is called with a runner on first base and the pitch is still thrown and the batter (who’s batting out of order) hits a double that scores the runner from first. If the manager appeals, as soon as the play is over the play—the balk—is nullified. The batter is sent back to hit and the runner is sent back to first. The at-bat is not over yet; the team batting still has the chance to send up the correct hitter without any penalty."

I'm having difficulty following the logic here. The defensive manager is aware that the current batter is batting out of order. The batter hits a double that scores a run. However, a balk was committed during the pitch. It seems that the manager's appeal is only negating the balk and is not affecting the batter. It seems the best he can do is negate the balk and cannot get an out for the batting out of order. Is that the way you read this?