It really doesn't make sense to me. The general thing is that you make your application, telling them all about yourself and why you want the firearms. Then the police do what enquiries they need to do to verify what you say and make a decision. They check your criminal record, your permission, your referees, any intelligence on you from various bodies, your guns and security and also your doctor. There is a cost for every one of them. But the only one increasingly the applicant has to pay extra for is the doctor.
In effect, the cost you pay for the certificate is a payment for the enquiries and admin they do to issue your certificate. So why the doctors enquiry is separate is beyond me. If the police say it's too much for them to afford, then why don't they ask Home Office, nationally, simply put another ten or fifteen quid on the price of a certificate and be done with it. I'm not in favour of the price of grants/renewals going up, but at least you'll know where you stand. the police can then send the enquiry to your doctor with a payment of £15 and say (as a certain rabbit says) "What's up Doc?"
I'm sure it's not beyond the wit of Man to come up with a workable system.