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I am working from memory here, as I gave up on the Kindle App (on PCs) some time back, finding it too limiting, but I think it will only open books in ones Kindle Library (after associating the App with ones Amazon account). If I recall correctly it would, however, see books put into that library by, for example, the Kindle desktop application.
I don't think that even if the App only is installed (i.e. the desktop application is not present) that the App was able to be associated with the file types for double click opening in Explorer, and I think you are saying that is your experience.
It may be that someone who has both the App and the desktop application installed can add to or correct, from immediate experience, the above.
For me, anyhow, as my preference was the desktop app with its increased functionality and given the App's limitations (apart from it's nice reading presentation) I was led to just dumping the App as being more trouble than it was worth.
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