Modified home page query does not yield expected results

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And why do you think it should do anything else?

What you do is:

  1. You add your filter to modify default WordPress query, which is run on index page. Your modifications are correct – this query will select published root pages.

  2. Then you run get_posts with default set of params (see below) and loop through them.

Default params for get_posts:

$args = array(
    'posts_per_page'  => 5,
    'offset'          => 0,
    'category'        => '',
    'orderby'         => 'post_date',
    'order'           => 'DESC',
    'include'         => '',
    'exclude'         => '',
    'meta_key'        => '',
    'meta_value'      => '',
    'post_type'       => 'post',
    'post_mime_type'  => '',
    'post_parent'     => '',
    'post_status'     => 'publish',
    'suppress_filters' => true );

You should use default WordPress loop, if you already modified default query. So do it like this:

// this will iterate posts already selected by WordPress with its default query (modified with your filter)
while ( have_posts() ) {
    the_post();

    echo "<li><a href="". the_permalink() ."">". the_title()."</a></li>";
}