Yes, he could be in certain fanfictions. Fanfiction allows for a lot of creative freedom. Maybe the writer wants to show Jack's journey from being a Unicron fan to realizing the true nature of this evil entity. It can be a great way to explore character development. Or perhaps it's part of a more complex plot where Unicron has some sort of allure that Jack initially falls for, but then has to make a choice between his newfound interest and his loyalty to his Autobot friends.
One reason could be the allure of power. Unicron is an extremely powerful entity, and Jack might be attracted to that power. Maybe he feels that the Autobots' power is not enough to deal with the threats they face, and he sees Unicron as a potential solution. Another reason could be a sense of rebellion. Jack might be tired of the Autobots' rules and way of doing things, and Unicron represents a break from that.
No, Transformers Prime is an animated series and doesn't have the ability to 'watch' fanfic. Fanfic is something created by fans for fans to read, and the Transformers Prime entity doesn't have the sentience or function to engage with such written works in the way a human or a sentient being capable of reading would.
The novels are important for the franchise as they offer different perspectives. They can tell a story from the point of view of a minor character, which can be really interesting. Moreover, they can fill in the gaps between different installments of the movies or shows. For example, if there's a time jump between two seasons of an animated series, a novel can explain what happened during that time. This helps to keep the overall story of the Transformers franchise more cohesive and engaging for the fans.