In my experience the epub-renderer defaults to a larger font than the kepub/pocket-renderer. Therefore if you go back and forth between them you will notice an annoying difference.
I wished the settings (that it remembers) was per renderer.
Back when I asked about this some years ago I think davidfor gave a tip that you could set the font-size to something below 1.0 in Calibre. That way everything that was transfered (as epub) to the Kobo got automatically adjusted to the same as the kepub/pocket-texts.
With a bit of luck David will pop-up here, or someone else who actually knows what they are talking about, in contrast to me.
