Well, Naruto has had the advantage of learning from many great shinobi over time. He also has a unique bond with his friends which could potentially give him more strength. Minato, on the other hand, had a shorter lifespan to develop his powers. Naruto has had more time to grow and surpass his father in strength.
Well, it depends on the specific fanfiction. There are various interpretations out there. Some fanfictions focus on Naruto's growth after the original series and give him abilities like super - charged chakra control or the ability to nullify Madara's strongest jutsu. However, in the original canon, Madara is an extremely powerful opponent. But in fanfiction, the rules can be bent to make Naruto stronger.
Well, it depends on the specific fanfic. Some fanfictions might give Naruto an edge over Madara by, say, having him master some super - secret jutsu that completely nullifies Madara's powers. Or they could boost Naruto's physical and chakra capabilities to an extent where he can easily defeat Madara. However, in the original Naruto lore, Madara is an extremely powerful foe, but fanfic authors have the freedom to change the power balance as they see fit.
Well, in some fanfictions, Naruto might be considered stronger because he has access to more powerful forms and jutsus. He might have mastered the Nine - Tails' chakra in a more advanced way than Minato could. Also, Naruto has trained with many powerful shinobi, which could give him an edge in strength compared to Minato.
In fanfiction, Naruto can be stronger than Madara for multiple reasons. Some authors might want to subvert the expectations set by the original story. They could give Naruto unique abilities like the ability to manipulate time, which would clearly put him above Madara in terms of power. Additionally, it could be a way to bring in crossovers. For instance, if Naruto gains powers from another fictional universe, he could easily be made stronger than Madara. Moreover, the author may simply want to explore a scenario where Naruto is the most powerful character, and making him stronger than Madara is a step towards that.
One feat could be Naruto's ability to use Sage Mode more effectively. In some fanfictions, he might be able to maintain it for longer periods or use it in combination with his other powers more seamlessly. This gives him an advantage over Minato who didn't have the same level of Sage Mode proficiency.
There could be a shift from enmity to a begrudging respect. Madara has always been a powerful and feared foe, but with Naruto being stronger, Madara may have to accept Naruto's superiority. Naruto, on the other hand, would likely try to understand Madara's motives better and might try to reform him rather than just defeat him.
The fanfic could portray Naruto as having greater physical strength and endurance. Maybe he can take more hits and keep fighting, while Minato might get tired more easily. Also, Naruto's strategic thinking in combat could be shown as superior, allowing him to outwit Minato in battles.
One possible reason could be that Naruto has developed some new and extremely powerful jutsu in the fanfiction. Maybe he has found a way to combine his Sage Mode with his Kurama chakra in an even more efficient and powerful way that gives him an edge over Madara.