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To sideload a book as a kepub from calibre, either you are using the KoboTouchExtended driver, or you are doing a conversion to kepub and then sending that. By the sounds of it you have been using the KoboTouchExtended driver. To stop sending as kepubs, either disable that or uncheck the option that enables the conversion function in the driver.
Some of what you are seeing is the difference between how epubs and kepubs are handled. The epub renderer does not show popups for any links. The kepub renderer does for some. You are also seeing that the links in kepubs are easier to press than in epubs.
For kepubs, my quick test suggests that links that include the id or name (the bit after the "#" and I know it has a name, but I can't think of what it is) will show a popup. Links without this, do not show a popup.
Your test book does show that backwards links don't seem to show a popup. I suspect that is because for a footnote, there is commonly a link to return from the footnote. You wouldn't want a popup for that.
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