Regardless of seating and format, BYU has got to play their game and beat every team. They were given a bye and one less chance of losing early on. That benefits them and the other top teams. It is similar to NCAA Tourney play where they have the play in game, now. The team that didn't play has the benefit of really scouting them and seeing who is hot, who is banged up, and getting an idea what their opponent is bringing to the table and how to counter. San Diego didn't have that with BYU, outside of season play. BYU had a week to prepare for that game and just came out flat and fell into the hero ball trap. During the regular season, BYU played the majority of their games on Saturdays and rarely plays back to back unless they are in an early season invitational, like they will be playing in Hawaii. It was pretty much a routine weekly schedule for those teams that had a bye.
San Diego and the lower ranked teams came in with a chip on their shoulder because of past seasons of being called out for not putting money into their programs and playing up to the standards of D1 teams. I can't remember whether it was Mark Few or St. Mary's coach that called out the smaller WCC teams by name, but the message was heard loud and clear by teams like San Francisco, Pepperdine and San Diego. I agreed with what he said and how there were 2-3 teams that keep the WCC viable but he embarrassed coaches, ADs, and players by speaking the truth about the disparity of the league and how they were hurting the strength of schedule of the better teams that put money into their facilities, players, and recruiting better talent. I have seen a really big jump in teams that were notorious cellar dwellers and it seemed like there were no guaranteed wins.
I believe BYU ran into the perfect storm of having a really bad start and a competitor sick of being embarrassed and called 2nd tier team with high school gyms. They had that Cinderella team feel and were they were tough. Every BYU player that cut inside was getting hit and San Diego was playing smart and utilizing that inside game. I normally put Child's and Baxter's D as an advantage towards BYU but the front court of SD had everything they wanted because BYU didn't dare double down low, off of the SD guards.
Every upset in the tournament has been a different set of circumstances but this specific game had nothing to do with seating or format. It had everything to do with players making lazy passes, trying to play hero ball, and players that were not mentally in the game. Childs went on that little run but when they doubled him, the guards and SF went right back to poor jump shots and 3s instead of driving and getting fouled. SD were out for blood for that overtime game.