I'm not seeing any differences between the version direct from Standard Books and the epub version sent via the KoboTouchExtended driver. Attached are screenshots from my Clara HD of the same pages. There are no obvious differences. I also did the same on my Libra H2O with the same results.
From your screenshots, it looks like you might have different font settings for the two books. It looks like you have chosen the centred option for the justification, but, I'm not sure about other options. Or, are you using patches? Or the Modify CSS option in the driver?
In any case, I'm really not seeing any differences between the kepub download from the site, or using the epub and KoboTouchExtended driver.
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