The remaining Service catering personnel are there to supply the deployed catering requirements (with stewards acting as kitchen hands and "front of house" staff in the mess tents) and also to provide a pool from which to generate the AT air stewards. Rather than being scattered in ones and twos all over the RAF, Service caterers are concentrated in certain locations in order that proper military line management can be in place. Marham is one location that springs to mind, as was Linton on Ouse (although my knowledge there could be a bit out of date).
Messes can become PAYD even with Service staff - the Service staff work alongside the contractor's employees and put the cash in the tills! I guess the contractor must pay the Service in some way for the privilege of receiving some GFX manpower....