It seems the best place to learn about how Fees are set was to look at the advice given to GPs on the British Medical Association's website. While I was about it, I read the separate section on Firearms Licensing, and the role that GPs should play in the process which the BMA has now agreed with the NPCC and the Home Office.
This lays out the various stages within the FAC/SGC Application when the police notify your doctor that you've applied, and been granted a certificate at the end. There are a series of different markers (clinical codes) put on your NHS Online Patient Record at each point. I've just been through all this with Cambs a fortnight ago (ONLY 12 DAYS AFTER MY FAC EXPIRED!

), so have watched all these alerts pop up on my medical record. There are at least a dozen of these in code, and plain language.
As we all know, completing the medical proforma isn't part of a GP's contract with the NHS. The legal responsibility for it lies with the senior doctors within the practice, which is usually one of the practice partners. This is a medical assessment of the patients medical condition so is classed as a factual statement taking 15 minutes of the Gp's time, or 20-30 minutes if it's not straight forward. His or her liability for signing it is now covered by the standard NHS indemnity. I paid £50, which seems to be the standard amount in this County. Methinks the fee goes direct to the GP principal who signs the form rather than the practice.
The practice may also add VAT to the fee, as any service provided by doctors is to enable a third party organisation to decide a course of action is subject to VAT according to HMRC. The BMA say it is working on a fees calculator for practices to use, so those FAC/SGC applicants who renewed some time ago might have a shock on their coming renewal.
In addition to confirming the applicant's own declaration that he/she isn't suffering from,or being treated for any of the 'notifiable' medical conditions, there are ten times as many other conditions assigned an NHS clinical code which trigger an indicator automatically on the patient's online record. I don't know what these are, but reporting them to the police is left to the GP's discretion. I'd advise anyone reading this to bookmark the links at the bottom. The concluding bit of the 1st link sounds ominous:-
"The list above is not intended to be exhaustive. Doctors should consider any other mental or physical condition which may affect the individual’s safe possession of a firearm or shotgun, now or in the future.
See also sections 3.34 and 3.35 when a patient has been subject to the provisions of the Mental Health Act 1983 and/or the Mental Health (Care and Treatment) (Scotland) Act 2003.
A specific list of diagnoses and conditions of around 100 items is being used to underpin the code writing for the computer flagging system."
We set out the BMA position on firearms licensing and what to do when someone applies for a firearms licence, including responding to the police and conscientious objection.
www.bma.org.uk
This page runs through considerations you should take into account when laying out the fees you can charge as a doctor.
www.bma.org.uk