Considering that Kavita's own FAQ has the following, it seems like even the author acknowledges that the two are not playing in the same space:

• Q. I really like Kavita, but can it mirror or just use my folder structure?
• A. No, Kavita uses filenames for parsing and is not designed for using folder structure. Please don't ask for this feature, it will never be implemented. If this is important to you, Ubooquity can be used and delivers this experience.