Yes, you can do this easily (if I understand your question that is!)
If you protect the folder content (say d:\data\inetpub\wwwroot\php) with an ACL of AUTHENTICATED USERS then all accounts in the master domain will get access after they have answered the browser user name and password dialog box.
You shouldn't have to do anything in your php code to do this. If you would like, though - you can simply include this snippet:
if (!isset($REMOTE_USER)) {
header("401 access denied");
// done!
}
at the top of any page that requires authentication fro an NT acct.
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