Actually, the USAF said the total life-time program cost differential was GREATER than 1%... which, according to the rules of this iteration of the contest, meant that capability above the minimum required was NOT to be considered.
Apparently, Boeing's operational costs were enough lower than EADS' to compensate for the higher initial development cost by more than 1% overall.
There were always going to be 4 developmental aircraft and 175 production aircraft no matter which aircraft won.
I doubt that running costs would have played much role in "how many hoses are in the air" on any given day... reliability and "mission capable availability rates" rule that equation.