First off, you're being extremely vague.
What kind of pickups are you talking about?
Jazz? Precision? MusicMan? What?
Second, pickups are not made to "look cool", they are made to convert the vibration of your strings into an electrical signal that can be amplified to produce sound.
I doubt that any pickup manufacturers are setting their pole piece height to "look cool". They are setting them to sound good.
Third, it's quite inconvenient to have pole pieces that protrude above the covers. You bump into them when you play, and if they aren't grounded properly, they will give you a buzzing sound when you touch them.
I have seen people go as far as to lay a strip of electrical tape over their pickups to avoid touching them.
Some people even prefer to cover the pole pieces entirely with blank covers, or even choose pickups with rail style pole pieces, so they will not be visible or exposed.