Not sure on sideloaded, I only use the kobo app for store bought books
It's not really a pop-up, it looks more like its embedded into the top part of the page, hard to explain but it looks like its part of the page, it only appears when you tap the page to bring up the controls, then goes again while reading
I usually only tap the page when finished reading, so I can hit the back button to go back to the home page, so its quite easy to ignore
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