I suspect from your inadvertent cough that perhaps some tourney organizers are not as diligent at checking requests against rankings.
I can't speak to what tourney organizers do; the ones my son has played in have seemed fairly well-balanced, but if you're a Flight 3 team playing a top-60 team in a tourney, either they didn't have enough teams to make the bracket remotely fair, or something is very bad in the match-ups. Our club's top 2011 Boys team (my son's age, the team above his) is around top-100 in CA, and plays in the NPL bracket (and when possible, plays in "higher-level" tournaments with mainly other teams in the top 100 ish). Those teams would generally beat Flight 1 teams, and crush teams below Flight 1.