This plugin hides all WP versions from the head of the document and anables auto updates. It could be placed in /wp-content/mu-plugin folder

cd-hide-wordpress-version.php

<?php
/**
 * @package CD Hide WordPress Version
 * @version 1.0
 */
/*
Plugin Name: CD Hide WordPress Version
Plugin URI: http://wordpress.org/extend/plugins/#
Description: This plugin removes the version number from WordPress pages
Author: Carlo Daniele
Version: 1.0
Author URI: http://carlodaniele.it/en/
*/

/** 
 * Filter whether to automatically update core, a plugin, a theme, or a language.
 * Defined in /wp-admin/includes/class-wp-upgrader.php
 * The dynamic portion of the hook name, `$type`, refers to the type of update
 * being checked. Can be 'core', 'theme', 'plugin', or 'translation'.
 *
 * @param bool   $update Whether to update.
 * @param object $item   The update offer.
 * 
 */
add_filter( 'auto_update_core', '__return_true' );
add_filter( 'auto_update_theme', '__return_true' );
add_filter( 'auto_update_plugin', '__return_true' );

/** 
 * Filter the output of the XHTML generator tag for display
 *
 * @param $generator_type string The generator output.
 * @param $type string The type of generator to output. Accepts 'html', 'xhtml', 'atom', 'rss2', 'rdf', 'comment', 'export'.
 * 
 * @return string $src
 *
 * @link https://developer.wordpress.org/reference/hooks/the_generator/
 */
function cd_remove_generator() {
	return '';
}
add_filter('the_generator', 'cd_remove_generator');

/** 
 * Hide WP version strings from scripts and styles
 * 
 * @param string $src The source URL of the enqueued style
 * @return string $src
 *
 * @link https://developer.wordpress.org/reference/hooks/style_loader_src/
 * @link https://developer.wordpress.org/reference/hooks/script_loader_src/
 */
function cd_remove_script_style_wp_ver( $src ) {
	global $wp_version;

	// parses query variables into string
	$query_string = parse_url( $src, PHP_URL_QUERY );

	// store variables into $query array
	parse_str( $query_string, $query_vars );

	// check if script version is equal to WP version
    if ( !empty($query_vars['ver']) && $query_vars['ver'] === $wp_version ) {
        $src = remove_query_arg( 'ver', $src );
    }
    return $src;
}
add_filter( 'style_loader_src', 'cd_remove_script_style_wp_ver' );
add_filter( 'script_loader_src', 'cd_remove_script_style_wp_ver' );

Hi @carlodaniele,
I don't know if there is any incompatibility with the latest version of wordpress (5.4.1) but I recently used this mu-plugins, and it happened three times that after a few hours or at most 1 day, there were automatically update all wordpress plugins, except the plugins that have been updated for a few hours.
It also happened having activated the "WordPress Auto-updates" plugin by setting everything manually.

This is the only mu-plugins I used, I deleted the folder, and after a few days it hasn't happened to me anymore, even by deactivating the "WordPress Auto-updates" plugin.

I hope it will help to solve the problem.

Thanks anyway for creating this plugin.