Generally, speaking, in these situations you should create a redirection from the alias to the canonical domain name. Otherwise you will be penalised by search engines since you have two domains with identical content. You can do that with Admin Tools' .htaccess Maker.
Beyond that, Admin Tools does protect your site regardless its domain name. The only place where we use the domain name you enter in the .htaccess Maker configuration is when we are redirecting between domain names or from HTTP to HTTPS (the latter because in some rare configurations the HTTP and HTTPS domain names are different).
No site protection feature in Admin Tools depends on the domain name at all.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!