I hope that we don't have a Language based Misunderstanding here. You say: "why would changing the player setup prior to the race effect pit time" If you, for Example, set the Pit Stop Strategy to let's say "refuel 15 L at Stop 1" and the default is refuel 60 L. Than it is obvious that the AI will refuel 60 L, but you only 15, there you have the Difference. That is why i have said that you have to use fixed Setups to get it equal. But i fear that @Herve_Versabeau didn't set it up properly or it is really bugged with Time based Races, like @Lazza did mention.
@Herve_Versabeau After 18 Years of Testing rFactor i'm more than a bit tired to do it Nowadays. But maybe, when i'm too bored one Day, i will start a Test with this.