I did some I-have-no-idea-what-I'm-doing sleuthing and think I have figured out what is causing the word spacing discrepancies:
The fonts aren't set to exactly the same size in the kepub and epub renderers. That is, I don't think that the "unify font size" patch makes both sizes exactly the same?
I zoomed in to the two screenshots and noticed that there is a slight shadow around the kepub's text (most discernable around the upper edges of 'T') which suggests to me that the font is scaled ever so slightly larger than the epub's thus causing "afterglow" to not fit on the same line.
This might also have a very minute effect on C (line spacing), as well?
Of course, the programmers know exactly what is going on with that patch and can let me know that my guess is wrong.
(kepub on left, epub on right - zoomed 1000%)