Easy peasy!
$args_for_query1 = [
'post_type' => 'custom_project',
'post_status' => 'publish',
'meta_query' => array(
array(
'key' => '_thumbnail_id'
)
)
];
$args_for_query2 = [
'post_type' => 'custom_project',
'post_status' => 'publish',
'meta_key' => '_thumbnail_id',
'meta_compare' => 'NOT EXISTS',
];
$query1 = new WP_Query($args_for_query1);
$query2 = new WP_Query($args_for_query2);
$wp_query = new WP_Query();
$wp_query->posts = array_merge( $query1->posts, $query2->posts );
$wp_query->post_count = $query1->post_count + $query2->post_count;