I wasn't sure which part was keeping you out until your second post. The instructions for disabling Admin Tools from outside Joomla! are here:
https://www.akeebabackup.com/documentation/troubleshooter/atwafissues.html.
It is probably the secret URL parameter on the first tap of Configure WAF that is keeping you out. With that enabled, you have to access the administrator login in the format www.mysite.com/administrator/index.php?secret.
As you figured out, the popup user ID and password prompt are controlled by the .htaccess and .htpasswd files in /administrator.
Dale L. Brackin
Support Specialist
English: native
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!
????
My time zone is
EST (UTC -5) (click here to see my current time in Philadelphia, PA)