Unfortunately, Kavita follows a rigid file structure on purpose. Joe has said he wants it to work this way. However, you can use the "Save to Disk" feature in Calibre to specify a custom file structure for Kavita so you don't have to do it manually.
Here is the Kavita wiki article on how to do this: https://wiki.kavitareader.com/guides/external-tools/calibre/
This is super helpful, I wonder if Calibre-Web uploads can be handled this way too.
From what I remember I'm my time using Kavita, basically the only way it knows what anything is comes from the file structure. It's called out pretty explicitly in the docs for example.
Now it's been a year or so for me so maybe now there are options to define your own structure or pick from some but I don't remember any.
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