Stress resistance. The long term results of lasik and prk are approximately the same. But prk gives a more solid front of the eye less resistant to pressure changes and trauma. For most civilian activities it makes no difference. The military requires pilots to have prk when needed to prevent any possiblity of problem and this may hold true in some circumstances for civilian flight.
Flaps. Prk may be preferred by some airline companies due to perception of flap complications, or postop halos or dryness but that also can occur with prk. Many commercial pilots have had lasik, and ilasik has even been approved for nasa astronauts. The commercial airline(s) of interest may have specific reasons they can share with you.