In 1 bid conferences, you want your best to get the auto bid. Maybe this doesn't 100% apply to the WCC because Gonzaga would always get a at large bid anyway, but you really don't want upsets in the conference tourney. You want your best in the dance.

This gives the best of both worlds. Fewer chances for your best to lose in the conference tourney with a bad loss that hurts their at large chances. Even a win can hurt NET or SOS numbers. But it also gives the chance for anyone to win their way into the tourney, even if it is much harder.