If a "normal ebook site" is one that allows you to download an ebook from their store without using their app, then Kobo is one. Just go to the store in a browser, login, go to the library and you should be able to download the book from there. You might need ADE if it has DRM, but that is normal for an ebook store.
But, there is no direct connection between the Kobo apps and calibre. You can explore the file system and find the book without to much trouble. The books are stored unpacked so you need to rebuild them to use elsewhere. And you would need to handle any DRM. It's a lot simpler to download from the store.
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