I think you got it wrong.
It doesn't matter where the transpoder is located because when you pass the loop it sends a signal to the pc giving you a lap. That means since both cars pass the loop at the same time (transponder wise not how we look at them) the result will be the same. That is the case for timming qualifings where everyone is running against time.
On finals now, where we run against each other, the car that has the transponder in front has the slight, not even whole second, advantage on other cars becuase it passes the loop earlier, BUT this is only the first lap. On the next laps it doesn't make any difference.
I hope I explained what I think is the case good enough!