Here is another workaround as a handy bash function passing the output of ebook-convert to gs, it preserves the outline:
Code:
topdf() {
local in=$1 tmp=${1%.*}-tmp.pdf out=${1%.*}.pdf
ebook-convert "$in" "$tmp" --output-profile=ipad \
--change-justification=justify
gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook \
-dNOPAUSE -dBATCH -sOutputFile="$out" "$tmp"
rm "$tmp"
}
Just run it as topdf <input-file>