At that time, the exchange was a second-price auction, and all parties could submit up to two bids (presumably, the top two bids from their own collection of advertisers). Let's call the Google bids G1 > G2.
Since Google already implemented automated bidding strategies, they would submit to this auction (1+a)G1 and (1+b)G2 for certain fixed small value parameters a,b. Project Bernanke computed on historical data the optimal values of these a,b parameters.
Cue government discovery misunderstanding documentation