The thing is that not only the sprites or music are protected, but also the names and characters, for example, Superman.
If you draw Superman from scratch and place that drawing in your game, it is still Superman, which is copyrighted content, it doesn't matter if you drew it from scratch. Drawing it from 0, by you, does not give you the legal right to sell or distribute said content.
As @Eris Lord Freedom says, it would have to be a "Transformative" work, for example, a superhero who flies, but who is not called Superman and who is not so similar.
When you make a fan game, it usually refers to names and content that is the property of a company, even if you create the sprites or music.
You can create a VN about a mustachioed plumber and a princess in a fictional world inhabited by turtles and you'll legally be safe.
But can it be considered a fan.game?
The moment you make a VN of Mario and Peach, what would be a fan-game. You also have a copyright problem, because that Mario and that princess are protected content.
As you say, there are certain lines that are not clear and could only be resolved in court. But in this case we are talking about Itch. If you make a VN with Mario and Peach and Nintendo comes with a DMCA to Itch.
What do you think will happen?
It is based on that that I always consider and recommend considering that any fan-game can be removed from Itch if the rights holder wants.
PD:
For example this case of harmony gold against argentine developments (sorry, only found in spanish)
https://www.guioteca.com/anime/harmony-gold-censura-produccion-de-fanaticos-arge...
This person had created some videos that told a fan-fiction story of an anime called "Robotech" all the content created from 0 and still had to delete everything.
He could have changed the name and designs, in such a way as not to use protected content, the problem is that by doing that, the product cannot be directly related to "Robotech" and therefore it would have ceased to be a fan-fiction of "Rototech".