You get exactly the features you want, and don't end up paying for features you don't need or want.
Auto dealers tend to stock vehicles with broad appeal. Those features may or may not be what you're after. If you tend to stray from the crowd in your tastes, pre-ordering may be for you.
You will be driving your car daily in most cases. It makes sense to get the features you find most necessary and desirable.
Thinking through what you really want reduces the urge to purchase on impulse, or to settle for something that's not exactly what you want.