If you think the pilot pay system is bad, just ask one of the flight attendants. Their pay system was so convoluted no one could figure out what they were supposed to be paid.
The systems they have in place are designed to underpay everyone. They make it has difficult as can be so people get frustrated of the fight and just give up. If a certain percentage of the employees either doesn't check their pay, or gets tired of the fight, it's free money for the company.