All of this can be handled by not allowing "future" substitutions. If the coach wants his DP to play defense for his flex, then he should inform the umpire when his team moves to defense.
What if you were to allow such a substitution, and allow a courtesy runner for the "future pitcher" and then the coach turns around and reenters his flex to start the bottom of the inning? Then you've just allowed a courtesy runner for a regular batter.
I agree with those that say the line up is official as accepted during pregame conference. The pitcher for the visiting team who is listed in the line up must pitch in the bottom of the inning, and has the right to a courtesy runner in the top of the inning.
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