The most reliable way I've found to get good PDF output from Eeschema under Linux is to first export to PostScript (File > Plot > Plot PostScript) and then use the ps2pdf command from ghostscript to convert to PDF. (The Arch wiki has a good writeup on `ps2pdf`.)

The biggest problems with this are:

1. It’s a lot of typing to get the conversion to happen (the minutia of which you won’t have memorized).
2. It leaves you with both a PostScript and a PDF of the document(s), one of which is likely to get out of sync with the other, which may or may not be in sync with the actual schematic, etc.

To help with this, I use the script below. I drop a copy of it into the root of a KiCad project and edit the OPTIONS as needed for the project. Then whenever I want PDFs of my schematics, I export PostScript from Eeschema and then click on this script in my file manager. Note that running this script will destroy any *.ps files in the directory—that’s by design.

makepdf

#!/bin/bash
 
# DESTRUCTIVELY convert all postscript files
# in working directory to PDF.
# Requires ghostscript.
 
# Mithat Konar 2013 (http://mithatkonar.com)
 
OPTIONS="-dOptimize=true -sPAPERSIZE=11x17"
 
FILES=$(ls -1 *.ps)
 
for file in $FILES
do
  ps2pdf $OPTIONS $file && rm $file
done

I’ve not tried the script on PostScript files other than those produced by Eeschema, but I’ve got no reason to think it won’t work on other PS files as well.