List all native posts in template page?

There is nothing wrong in your query, but there is some code (a plugin?) that remove from results the posts in the category having term id 1 or 4. (Normally category with term id 1 is ‘uncategorized’)

You can notice that looking at request performed

AND ( wp_posts.ID NOT IN (
  SELECT object_id FROM wp_term_relationships WHERE term_taxonomy_id IN (1,4)
)

and at 'category__not_in' query var:

'category__not_in' => 
    array (size=2)
      0 => int 4
      1 => int 1

Now its seems that category__not_in argument is added using pre_get_posts action.

If my guess is correct, you can try to remove all actions from that hook to prevent any query modification:

global $wp_filter;
$pgp_hooks = FALSE;
if ( isset( $wp_filter['pre_get_posts'] ) ) {
  // save hooks
  $pgp_hooks = $wp_filter['pre_get_posts']);
  // remove hooks
  unset( $wp_filter['pre_get_posts'] );
}
// set 'suppress_filters' param to true to skip sql filters
$args = array(
  'posts_per_page' => -1, 'post_type' => 'post', 'suppress_filters' => true
);
// query
$all_posts_query = new WP_Query( $args ); 
// reset hooks after query is performed
if ( $pgp_hooks !== FALSE ) {
  $wp_filter['pre_get_posts'] = $pgp_hooks; 
}
// loop goes here...

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