Have mu-plugin remove meta box ONLY if it isn’t already removed in functions.php

Hmm, a lazy workaround—as long as you’re not running PHP < 5.3.0—might be to use a namespace in your mu-plugins file.

Something like this might do the trick:

<?php
namespace Arglebargle;

\add_action( 'wp_dashboard_setup', 'Arglebarle\remove_x_widget' );

function remove_x_widget() {
    // If the meta box has already been removed, it shouldn't be an
    // issue to 'remove' it again.
    \remove_meta_box( 'x_dashboard_widget', 'dashboard', 'normal' );
}

This code is untested. I hope it provides a good starting point.