Most apps that close when the windows closes are not document-oriented apps. For them, there is only one window and one function. The calculator app you mention

Most apps that close when the windows closes are not document-oriented apps. For them, there is only one window and one function. The calculator app you mention is a good example. Once you close that window the app has no other purpose it is setup to auto-close the app. Document-oriented apps expect that, after you close the document, you might want to open another one or start a new document. Documents <> Apps