Thing is, a race car is designed with the fact in mind that
you're not going to do anything but drive when you're in the seat. If there were racing-while-talking-on-cellphones competitions, the automatic transmission would probably be a better optimization in terms of available-attention-to-performance.
Likewise, for some types of programs (extremely parallel ones, for example), you have so many high-level considerations that also thinking about the low-level implications would simply be too much. Premature optimization is just as much a drain on the programmer as the program.