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Apple has not changed since 2000 ie beginning of OSX - and is the same as NeXT from 1990.
The red button closes the window - if the app is a simple one and can only have one window then the app closes if can have multiple windows then the app stays running so you can open a new window - clicking on the dock icon puts the app menu on the OSX menu bar. There are two short cuts cmd-w to close a window and cmd-q to quit the app.
Also close is not the same as minimise - close removes the window. The point of this is that you are running virtual memory - there is no need to quit things - they just get swapped out to disk and an inactive running app has minimal effect on the rest, but if you click on it it responds much quicker than if it had to rerun from the beginning.
Windows, macOS each have their own way of doing things and Unix based on X11 has multiple possible desktops some of which copy Windows or macOS others do their own thing.
Calibre I think has copied the Windows way which is not how macOS and many Linux work. If it followed Apple guidelines it would be an app that had a window for each library. Or if you think of it as only having one library at a time but needeing to remain running (e.g. for server) - then like Apple music it would have a windows menu that would reopen the closed Window.
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