How can I output a php value into a JS file within WordPress?

PHP

wp_enqueue_scripts is a good time to localize the data. Make sure you target your script and create a name for the object as well as passing an array of data. In this case twitter_settings is the object that will be created and will hold all the data. twitter_settings.tweets_widget_id will ultimately hold your $tweet.

add_action( 'wp_enqueue_scripts', function() {

    // Get the current data
    if ( empty ( $tweet = get_theme_mod( 'tweets_widget_id' ) ) ) {
        $tweet="No Widget ID";
    }

    // Localize script with data to `twitter_settings` object
    wp_localize_script( 'twitter', 'twitter_settings', array( 'tweets_widget_id' => $tweet ) );

    // Enqueued script with localized data.
    wp_enqueue_script( 'twitter' );
} );

JS

Access the localized data from the twitter_settings object

var config2 = {
    id: "" + twitter_settings.tweets_widget_id, // based on comments
    domId: "tw-widget2",
    maxTweets: 3,
    enableLinks: !0,
    showUser: !1,
    showTime: !0,
    showInteraction: !1,
    lang: "en"
};
twitterFetcher.fetch(config2);

Test

(optional) Test to make sure the variable came through ok.

<script>

    (function ($) {

        alert( twitter_settings.tweets_widget_id );

    })(jQuery);

</script>