It's a moot point. I doubt that every person who does the W.O.D. does it the same way. I suspect the folks here will post the W.O.D. knowing full well that people will modify and adapt it to their specific needs. The W.O.D. the day is a suggestion, not a commandment written in stone.
Besides, your buddy is preparing for a specific need. His point about working weaknesses is valid when there is a specific goal, e.g. squatting, bench pressing, deadlifting strength. Crossfit seems to be more about all-purpose fitness, not specific strength.