Most chief pilots negotiate their own salary. That's the way it was at Delta when I did an internship in the chief pilot's office. If they just got paid what equipment they could hold, why would anyone do it? Come to work every day or get half the month off? Although I'm pretty sure I make more than our chief pilot with the overtime I'm flying.
I'm on my third airline, and all three of my chief pilots have been great. They don't have as much power as you may think, it's more of a required position the FAA makes airlines have...