I see, I don't use the “Library Browser” that often. But I am not aware that you can delete the factory library in the library browser or organize it into folders. You could send a feature request here:
Feedback - Logic Pro - Apple
Some parts of the library are easier to find than others. Some are visible in your Mac's Library folder, others are hidden in the app itself, like the “Darkened Theater” patch:
Logic Pro.app/Contents/Resources/Patches/Instrument/Piano/z01 Processed/Darkened Theater.patch
If you change the contents of the app, you risk losing the functionality of the entire app, and any editing will be overwritten with a new Logic update.
However, it's possible to save and organize the user patches by pressing Save... in the lower right corner of the Browser.