Goku being born with SSJ4 in fanfic would likely make him a force to be reckoned with from infancy. This could result in quicker power-ups, different battles, and maybe even a shift in the balance of power among the characters.
One scenario could be that Goku surprises Beerus with his speed and initial attacks as SSJ4. But then Beerus counters with his hakai and forces Goku to dodge constantly. Another could be that Beerus underestimates Goku at first and Goku manages to land some powerful blows.
Well, in many fanfictions, SSJ4 Goku is often depicted as having a chance against Beerus. SSJ4 Goku has shown incredible strength and combat skills. But Beerus has the power of a God of Destruction. His hakai ability could potentially wipe Goku out. Still, if the fanfiction is written in a way that gives Goku some new power - up or a special advantage, he could win. It really depends on the creative direction of the fanfic writer.
It often starts with a shock or surprise at the mpreg situation. Then, they gradually learn to rely on each other more. For example, Vegeta might start to show a more caring side that he usually hides, and Goku might become more responsible. They'll have to communicate more, sharing their fears and hopes about the future with the baby.
Well, if they were brothers in a fanfic, it could change how they interact with the other characters. Maybe they'd have a deeper understanding and fewer power struggles between them. Also, their family background and upbringing could be explored in new and interesting ways.
It's a bit hard to say for sure. Both Vegeta and Goku have their moments of strength. Goku has some unique powers and techniques that give him an edge at times, but Vegeta is no slouch either and constantly works to catch up and surpass Goku.
Generally, Goku still holds the edge over Vegeta. Their power levels fluctuate, but Goku often achieves higher peaks of strength and unlocks more powerful forms first.