I'm happy to report that I got all the custom fonts working with epub, following the instructions on the wiki. Also I got rid of the huge gaps on the bottom by setting the widows and orphans to 0 in the stylesheet.
The Bookerly is working too, with both formats.
Now the epubs look really good. But I'll have to decide which format I want to use... The map in the epub can't be zoomed in, but the typography looks somewhat better (I use justified text). There's not much difference in speed, at least I haven't noticed so far. Reading stats and time left aren't important for me. Eh, decisions...
Btw, I installed some nice custom screensavers, while I was at it. Don't particularly care for book covers as screensavers.
Many thanks again to all who helped and instructed.
