The relationship dynamic is a major element. It's not a typical hero - villain or even a normal relationship. They might be partners in crime, or have a more complex emotional bond that goes beyond just friendship or romance. For example, they could be using each other for their own ends while also having some level of genuine feeling.
Another element is the changed world view. The fanfic usually presents a different take on the My Hero Academia universe. With Deku as a villain, the power dynamics, the perception of good and evil, and the overall story line are all altered. This new world view affects how Deku and Toga interact not only with each other but also with other characters in the story.
One key element is the exploration of their dark sides. Since Deku is a villain here, his usually heroic traits are twisted. And Toga's already unstable nature gets even more interesting when paired with him. There's often a lot of morally grey areas explored.