The KoboTouchExtended driver is doing it. The whole purpose of the driver is to transform epubs to kepubs. It does this without using the full conversion pipeline or adding the kepubs to the library. To turn this off, either go back to using the built-in KoboTouch driver or uncheck "Enable Extended Kobo Features" option on the fourth tab of the KoboTouchExtended driver's configuration.
But, I doubt you will see a difference between the kepub and the original epub. The spans do not have any styles. There are a couple of divs wrapping each paragraph. The only problem that could cause is if the stylesheet doesn't handle them properly.
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