Run differential is a terrible tie breaker. Not only for the reason states in the op. But the pool often comes down to who had less mercy on the worst team in the pool. If you pitch your worst pitcher and move your back up players into the lineup and win by 7. And another team keeps riding their horse and keeps all the regular starters in and wins by 15. They get rewarded.
And yes the rules of the game are the rules. But in pool play the "game" is stretched out to be all the games equal one game when run-diff is looked at as the main tie breaker.
Most of the time when we see run differential it's capped at 8 so you can't run up the score. Always pick away in these tournaments. I actually like this tiebreaker as it allows you to throw some newer pitchers in without the 3 runs they allow killing you.