Top Level ,htaccess modification/protection when WP installed in subdir

I have my WordPress multisite installed in a subdirectory. iThemesSecurity makes its modifications to the .htaccess file in the subdirectory. I have a very small .htaccess file at the top level (basically it just points users to the subdir by default). I am concerned that the top-level .htaccess file represents a chink in my security armor. Is iThemesSecurity checking for this kind of situation and/or already taking steps to protect that higher level .htaccess? If not, what manual steps should I take to protect my website?