In such a fanfiction, perhaps Luffy would convince Nami to join his crew much sooner. They might start their adventure earlier, exploring uncharted islands together. Maybe they would form a stronger bond right from the start, sharing their dreams more openly.
In this fanfiction, an interesting plot point might be that Nami's past with Arlong is revealed to Luffy earlier. This could lead to Luffy taking on Arlong much sooner in the story, changing the whole sequence of events. Also, their early meeting could mean that Nami is more confident in Luffy's leadership from the start, and they might recruit other crew members in a different order. For example, they could meet Usopp earlier because of their different exploration routes due to the early bond between Luffy and Nami.
I recommend One Piece: The Great God Usopp to you. This book is a story about Usopp. It tells the story of how he obtained the League of Legends system through an accidental transmigration and became invincible. If you want to read a One Piece Doujinshi novel with a deceptive cloth as the main character, this book is perfect for you. I hope you will like my recommendation.
Their dynamic might change as they become more reliant on each other. Luffy has always trusted Nami's navigation, but over the two years, he might start to seek her advice in other matters too. Nami, on the other hand, may become more confident in Luffy's leadership and be more willing to follow his crazy plans without hesitation.
Perhaps in this fanfiction, their relationship deepens over the two years. They start to understand each other on a more personal level. Nami might become more open about her past traumas with Luffy, and Luffy, in turn, shows her more of his vulnerable side. This could lead to a stronger bond between them, not just as nakama but also as two people who truly care for each other.
Friendship turned to more is a very common theme. Since they start as crewmates with a normal friendship in the original, fanfictions often explore how that can develop into a romantic or deeper emotional bond.