The parking configuration is surely optional, and it's used only to fix eventual conflict with other scenery object that you cannot remove.
The airplane configuration is NOT optional, and it's required before you can do anything in GSX with an airplane. Without it, all door positions will be likely wrong, especially those not on the main passenger door.
Be sure all your doors are set correctly in the airplane customization page, and configure the parking only in case there's a scenery object in the way from the vehicle default starting position and the airplane door.