Clear out some default WP settings on new installation.

wp_init_cleanup.php

<?php

/* modified from https://code.tutsplus.com/tutorials/how-to-activate-plugins-themes-upon-wordpress-installation--cms-23551 */

// set the options to change: https://codex.wordpress.org/Option_Reference
$option = array(
    'blogdescription'               => '',
    'comments_notify'               => 0,
    'default_comment_status'        => 'closed',
    'default_ping_status'           => 'closed',
    'default_pingback_flag'         => 0,
    'moderation_notify'             => 0,
    'start_of_week'                 => 0,
    'medium_size_w'                 => 768,
    'medium_size_h'                 => 768,
    'permalink_structure'           => '/%postname%/',
    'blog_public'                   => 0,
    'gzipcompression'               => 1,
    'use_smilies'                   => 0
);

// update the options
foreach ( $option as $key => $value ) {
    update_option( $key, $value );
}

// flush rewrite rules
global $wp_rewrite;
$wp_rewrite->flush_rules();

// delete the default content
wp_delete_comment( 1 );
wp_delete_post( 1, TRUE );
wp_delete_post( 2, TRUE );