[memeplex]

Here is another workaround as a handy bash function passing the output of ebook-convert to gs, it preserves the outline:

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>