Creating an image like that is a good idea, and, there is no reason not to do it. But, it doesn't completely solve the issue of a factory reset. The factory reset restores the original firmware from the recovery partition. Unless this is also updated, after a factory reset, a Mini will start with a much older firmware version.
But, at the moment you don't need to use the Kobo desktop application. The appropriate firmware version can be downloaded and manually installed. I usually mention this when posting a message like the one above. If you download and keep a copy of that, you should always be able to restore it. Plus, while Kobo do not officially support the Mini with more recent firmware, they do work. A lot of people are upgrading the Mini to these firmware versions manually with no issues.
Also, I don't see Kobo dropping support for the Mini in the desktop application any time soon. Based on their past behaviour, they are very slow at doing things like this.
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