I'd speculate that PAD probably commands a higher fee than most of the other Trek writers, due to his relatively high-profile in the comic book world, so if they're cutting costs, it stands to reason they'd be using him less.
I don't know if this is still the case, but back in the 90s it was PAD's success in Trek novels that was leading to a higher fee in other areas like comic books. He was far better known for his New York Times bestselling Star Trek novels than he was his work on the Incredible Hulk or X-Factor.
These days that might not be the case, but other than his work adapting the Dark Tower I can't think of any big seller he has written in quite sometime. He is popular with fans and very talented, but comics don't sell like they used to and Peter David was never quite a best seller.
If I had to guess, PAD would be more expensive because of that previous Star Trek success, much like Timothy Zahn and his Star Wars novels, if he truly does command a higher rate than someone like David Mack which I'm not sure is the case.