OK, now I'm going back to yesteryear when I was a player-coach to see how I could possibly use this rule advantageously. I tried that a lot, manipulating rules.
In the modified and fast pitch games, if I was the defensive coach and the OP situation played out, I might try this. If I was aware of the BOO at the time.
When the BOO was noticed, I'd get the infielders together and put this play on. Intentionally walk the BOO batter, but on ball four, oops!, throw a wild pitch. Maybe we'd get lucky and grab an out if the runner tried to score from third base. If we get the out, bonus. Outs will stand. Even if the runner scored, it was a result of the BOO batter becoming a BR. Now appeal the BOO before the next batter.
The correct batter would be ruled out.
The runner from third (if s/he scored) would be returned to third. If out, remains out.
The BOO batter's time at bat would be negated, and the correct batter would then come up to bat.
Course I'd need an umpire who knew this rule better than I did in order to pull it off.