I beg your pardon, the ebook that I had tested was
David Copperfield.
I always set the Kobo to justify the text.
Here are a few examples of different formatting between the KE>(E)>KE and the K versions of the ebook (I have only checked the first dozen of pages):
The differences involve line spacing and consequently the final number of lines per page (the kepub sento to Calibre and reconverted through KTE - aka KE>(E)>KE - produces thinner line spacing => more lines per page).
Of course I do believe in the lack of issues in Greatest Expectations, as I re-affirm that I didn't find any differences in Star Born just like you reported.
(It could well be that they got David Copperfield's kepub completely wrong - as JSWolf suggests - and that I'm just being a dumb idiot...)