The Point of Using apply_filters()

The point is to allow developers to customise aspects of your theme or plugin.

When calling apply_filters() you provide a name and a value that you want developers to be able to filter.

For your example:

$array = apply_filters( 'du/class/method' array(
    'index'    => 'value',
    'index'    => 'value',
    'index'    => 'value',
    'index'    => 'value',
) );

Developers can now change the value of $array in your plugin by using the du/class/method filter with add_filter(). To add an item, perhaps:

function wpse_303378_filter( $array ) {
    $array[] = 'New item';

    return $array;
}
add_filter( 'du/class/method', 'wpse_303378_filter' );

The name of the filter, in this case du/class/method can be whatever you want it to be, but many developers will ‘namespace’ it so it doesn’t conflict with any other plugins. Advanced Custom Fields, for example, prefixes all its hooks with acf/. Your example implies that the filter name uses the class and method that it occurs in as a way to group related filters, but it will depend on the plugin.

You can read more about filters here.