How have I misconfigured basic auth for my wordpress site?

Ok editing the default-ssl.conf as described here (or in my case /etc/apache2/sites-enabled/mysite.com-le-ssl.conf) to add auth settings to the end of the Virtual Host block works fine now.
So it’s now:

<IfModule mod_ssl.c>
<VirtualHost *:443>
    ServerName mysite.com
    ServerAlias www.mysite.com
    ServerAdmin webmaster@localhost
    DocumentRoot /var/www/mysite.com
    ErrorLog ${APACHE_LOG_DIR}/error.log
    CustomLog ${APACHE_LOG_DIR}/access.log combined

    Include /etc/letsencrypt/options-ssl-apache.conf
    SSLCertificateFile /etc/letsencrypt/live/mysite.com/fullchain.pem
    SSLCertificateKeyFile /etc/letsencrypt/live/mysite.com/privkey.pem
    <Directory "/var/www/mysite.com">
        AuthType Basic
        AuthName "Restricted Area"
        AuthUserFile /etc/wordpress/.htpasswd
        require valid-user
    </Directory>
</VirtualHost>
</IfModule>

The page also explains how to use .htaccess files by modifying AllowOverride.

I should probably comment on the guide I originally followed