Load front-page.php from subfolder

You can make use of the frontpage_template filter to adjust where your template should be loaded from

add_filter( 'frontpage_template', function ( $template )
{
    $locate_template = locate_template( 'page-templates/front-page.php' );

    if ( !$locate_template )
        return $template;

    return $locate_template;
});