I'll tackle this in bullet points.
1. I'm an Auburn fan (have family ties to it) and was upset to see them get shut out of that game.
2. Bowling Green did have an impact. Besides Utah and Boise State, BG was the best Mid Major team that season (9-3; finished ranked 27 in the AP Poll) and was a good SOS/computer ranking boost to anyone's schedule. When BG dropped Auburn and took a game with Oklahoma, it initially had a double impact. Auburn lost that good SOS/computer boost and Oklahoma got it. In the end, when the Sooners beat out the Tigers, it had an impact. A third impact was that Auburn replaced the 3rd best mid-major team in the America with a 1-AA opponent. 1-AA opponents can do nothing but harm to your BCS score.
3. The SEC was down.
http://www.usatoday.com/sports/sagarin/fbt04.htm
This is Jeff Sagarin's 2005-2005 rankings. The SOS of SEC teams is pretty low. Auburn's schedule is 60; LSU's is 46; Georgia's 41. Given that the bulk of their games were against SEC teams, it's reasonable, IMO, to state that the SEC was down that year. Auburn suffered from that in the computer rankings (note: OU's schedule was ranked 13 according to Sagarin that year).
In bowl games, ranked SEC teams did as follows:
LSU-lost to Iowa
Georgia-beat Wisconsin
Auburn-beat VT
Florida (not actually ranked, but 1st receiving votes)-lost to Miami