The final ratio is usually considered seperate from the main transmission, kind of like the front sprocket on a bicycle. Often it is actually on the other end of the driveshaft within the differential; I like to remember the term "4:11 posi", commonly assosciated with built muscle cars, as it refers to the lower ratio, higher leverage, positraction (extremely limited slip) differential gearset. Altering this ratio will trade top speed for acceleration in a very linear relationship, while leaving all the shifting gears relationships unchanged IN PROPORTION TO EACH OTHER. Obviously if you set your final to a top speed of 75mph, each transmission gear will have a very short climb compaired to a top speed of 150.
In an ideal circumstance, you would want to group your transmission gears in such a way that you could keep your engine in the powerband throughout the acceleration portions of the course. A typical gearset for a high horsepower narrow powerband engine might include a very tall first and possibly second gear, since the driver intends to never slow to these speeds, followed by several closely spaced gears, each intended to work just through the sweet spot, handing acceleration seamlessly to its slightly taller sibling, with the tallest topping out at redline at the end of the longest straight. The autoset is just what the name implies, it is a means by which you can approximate the gear grouping effect, it squeezes or widens the individual gear ratios without changing the final. Again, it should be obvious how this can affect top speed and acceleration. If you squeeze your gears to extremely narrow ranges for acceleration, you will quickly use them up and have nothing left for top end.