To change KomodoIDE to an external diff tool, the same diff tool that you have setup for Mercurial from the command line, you need to check a couple things in your hgrc file and then change one setting in Komodo.
Make sure you have the following settings in your .hgrc file:
kdiff3.args = $base $local $other -o $output
To make sure this works, type in hg kdiff3 and you should see kdiff3 open, showing your changes.
In KomodoIDE all you need to change is your Preferences -> Source Code Control -> Mercurial. In the Diff options, type in kdiff3.