... points to win the women's natty by placing 1,2,3, & 4 in the Women's 400m (and then of course they won the 4x400 relay).

That 39 points from women's 400m was enough to place them 4th nationally if they only sent those 4 athletes to the meet. (they sent more and took 1st with 63 total points

How does dominance in 1 event score you enough points to do that?

Seems to top heavy.

1 first place finish shouldn't equal eight eighth place finishes IMO. Maybe at smaller events with fewer schools, but the system breaks down at national meets where there are the best from dozen's of schools...