Karabiner → Preferences → Misc & Uninstall → Open private.xml
private.xmlを以下のように修正
private.xml
<?xml version="1.0"?>
<root>
<replacementdef>
<replacementname>EMACS_MODE_IGNORE_APPS</replacementname>
<replacementvalue>
Atom,
</replacementvalue>
</replacementdef>
</root>
Karabiner → Preferences → Cange Key → Reload XML
で反映