WordPress multisites is really not multiple sites. It's just smoke and mirrors. You have one, big site with some duplicated tables. The whole lot pretends to be multiple sites by using some trickery.
From the perspective of Admin Tools this is still one big site. The protection is at the fundamental WordPress level, before WordPress' multisite code kicks in. This means that the configuration is set globally, through the Network Administrator. All blocks also apply globally. Each individual network blog has no control over Admin Tools' settings. It should go without saying that the .htaccess Maker settings are of course applied globally since the entire blog network has a single .htaccess file anyway.
Nicholas K. Dionysopoulos
Lead Developer and Director
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