The default output format is set in the preferences. In the preferences dialog, go to "Behaviour" and then it is the first drop-down list. There is also a "Preferred input format order" that you might want to set to put AZW3 at the top.
But, what exactly are you doing when you produce the zip and other types of files? If you are adding book to the library, then claibre will add whatever format they are in. If you want an AZW3, you need to do a conversion after adding it.
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