In the comics, Thor was mainly portrayed as a physically fit and strong character. There might have been rare alternate storylines or interpretations where his appearance was different, but that wasn't the norm.
I'm not very familiar with this specific fanfic. However, generally, a fanfic about Loki and Thor might explore their complex relationship in the context of the Marvel universe. If Loki is intersex in this fanfic, it could add an interesting layer to the character's identity and how they interact with Thor.
When Thor is mean to Loki in fanfiction, it can lead to a downward spiral in their relationship. Loki, feeling constantly attacked, may lash out in more extreme ways. Thor, on the other hand, may double down on his meanness, believing it's the only way to deal with Loki. This can create a cycle of animosity where any love or brotherly bond they had is overshadowed by anger and distrust. For example, Loki could start to form alliances with Thor's enemies out of spite, and Thor would see this as confirmation of Loki's untrustworthiness, making the relationship even worse.
There's 'Thor's Redemption in Loki's Arms'. In this story, Thor realizes his true feelings for Loki after a series of events that nearly tear Asgard apart. It's a tale full of emotion and character development.
Thor might initially go into denial. He can't believe that Loki is truly gone. He may hold Loki's body for a long time, as if waiting for him to come back to life. Then, he could become angry. Angry at the situation, at whoever or whatever caused Loki's death. Eventually, he may find solace in the memories of Loki. Remembering the good times they had together and using those memories to move forward.