In the fanfiction, Thor could be a key factor in Loki's development within the TVA. Since Thor has always had a strong influence on Loki, his presence might make Loki question his actions and motives even more deeply. For example, Thor could remind Loki of their past, both the good and the bad times, which could lead Loki to make different choices within the TVA's framework.
Their interaction could also lead to a change in their relationship dynamic. In Asgard, Thor was often the more dominant and 'good' brother, while Loki was the troublemaker. In the TVA, they could become more equal. Loki might have knowledge about the TVA that Thor doesn't, and Thor could bring his strength and loyalty to the table. This new dynamic could be a turning point for both of their characters as they navigate the strange world of the TVA together.
Whether the TVA is bad in the comics is a complex question. Different storylines and character interactions can shape this opinion. Sometimes their intentions seem good but the outcomes might be controversial.
TVA can be found in certain comic storylines. The extent and nature of its appearance can differ based on the creative direction of the comic writers and illustrators. Sometimes it plays a significant role, while in others, it might have a more minor presence.
The TVA in the comics isn't strictly evil. Their motives and methods might be questioned, but it depends on how you interpret their role in the story's context.