Also in a sport where driver preference is significant to the cars overall performance, just because a system is theoretically faster on paper, driver preference for the way he drives the car may be affected by the new system causing him to drive slower than theoretically possible.
A situation that comes to mind is the beginning of the exhaust blown diffuser last year with RBR, where Webber had an advantage over Vettel in terms of car pace, and it wasnt until a throttle mapping change where the performance gap changed.
Also at Japan (IIRC) this year, RBR were trying a different suspension and their relative performance to Mclaren had dropped, and when Vettel suggested a revert to the tried and trusted he was able to put the car on pole the next day.
So in recap, when the system is chaotic in nature with driver preference an important factor, engineering numbers dont always represent the whole picture.
"I continuously go further and further learning about my own limitations, my body limitations, psychological limitations. It's a way of life for me." - Ayrton Senna