Yes, it can be. In fanfiction, Goku being born with God Ki can completely change the power dynamics. It could mean he starts off with a much higher level of power than in the original story, leading to different battles and interactions. For example, his training might take a different path as he already has this innate God Ki. He could potentially face stronger opponents earlier and form different alliances.
Well, Goku could enter the Game of Thrones world during one of his training sessions where he accidentally travels through dimensions. In this new world, he would find the concept of the Iron Throne and the power struggle very strange. But his nature would make him oppose tyrants like Joffrey. He might start his own 'Saiyan - style' kingdom where strength and honor are the main values. His interactions with characters like Tyrion would be interesting, as Tyrion is a smart strategist and could potentially learn from Goku's combat skills while Goku could learn about the complex politics from Tyrion.
In a Game of Thrones fanfiction, Goku's character would be a bit of an oddity. He would be constantly confused by the backstabbing and lies that are so common in the GoT world. However, his loyalty and determination would shine through. For instance, if he befriended Jon Snow, he would stand by him no matter what. His fighting style would be completely different from what the people of Westeros are used to. Instead of swords and shields, he would use his fists and ki blasts, which would make him a fearsome opponent in battles.
Well, Vegeta would be a likely character. He might be initially suspicious of the female Goku. Maybe he thinks she's a threat or just can't believe there's another Goku - like being. He could be there to add some comical moments as he tries to understand the situation.
In general, it's a bit of a toss-up. The strength of Manga Goku and Anime Goku can vary depending on the specific arcs and battles. Sometimes, it might seem like one is stronger in a particular situation, but that could change in another.
Another possible main character could be the villain that forces the two Gokus to meet. This villain could be a new, super - powerful threat that the two Gokus need to deal with. Their meeting becomes a crucial part of the story to defeat this powerful foe.
One of the characters who could betray Goku is Piccolo. Although they've been allies for a long time, in fanfiction, things can change. Perhaps an ancient evil force takes control of Piccolo's mind and makes him turn on Goku. Or it could be Krillin. He might be influenced by an outside force that convinces him Goku is becoming too dangerous. Also, don't forget about the Kais. If there's some sort of power imbalance or a threat they perceive from Goku, they might betray him to maintain the order of the universe in the fanfiction.