Yes, it is. As a 'Code Geass' fan, it gives you more content related to the series. You get to explore the story further and might discover new aspects of the characters and the world.
Code Geass did start as a manga. However, its anime version became even more widely known and beloved. The manga provided the foundation for the rich story and characters that were further developed in the anime.
Code Geass started as an anime. The manga was based on the anime's success and came after to expand the story for fans. Some elements might differ between the two, but the anime was the original form.
The 'Code Geass 5 Year Fanfic' might expand on the original world - building by delving deeper into the politics of the different nations. For example, it could explore how Britannia's rule has changed over the five years, whether there are new rebellions brewing in different regions. It may also focus on the economic aspects. Maybe some regions are suffering more due to Britannia's policies, and this leads to new forms of resistance.
One difference could be in the character relationships. Maybe in the original plans, some characters were closer or more hostile than in the final story. For example, the bond between Lelouch and C.C. might have been different.