"However, the Joint Council for Qualifications (JCQ), which represents the UK’s major exam boards, said that the introduction of a gender neutral option would not affect national trends since numbers would be too low to have an impact."
This is a guess.
They need to be clear what they are asking teh students to provide. If it's "gender" then they can all put boy / girl / neither it makes no odds.
This will render the stats iffy obviously. They say it won't be many - how do they know? How do they know how many boys will put girl and vice versa - they will not be able to tell if they're just picking whatever on the day. Many girls might pick boy with an idea it might have a positive impact on their grades...
For subjects with very low male or female uptake any skewing could also be non trivial.
Essentially they have decided to stop bothering with stats based on sex and move to a system with stats based on what people feel like putting on the day based on . How this will be beneficial is anyone's guess.