Call it a database if you wish. In fact it is probably sqlite running behind the scenes. It is a relational model, a different way of organizing things compared to the hierarchical model of the filesystem. There is probably enough literature about that to fill your ebook library ;)

I suppose that the "library" model is what most people prefer since most modern media apps use that in some form or another. Or maybe it is because of Steve Jobs reality distortion field ( https://oleb.net/blog/2012/06/steve-jobs-on-the-file-system/ ). Still, I hate all these apps attempting to hide the filesystem from me.