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When you add a directory exception, here's how it works. When you tell it to allow access to components/com_foobar/something then all contents of the components/com_foobar/something directory in your site's root and all of the contents in its subdirectories are accessible, except for PHP files.

Here's you to test it. First, create a small file called test.php containing this:

<?php echo('You should never see this message');

and upload into this directory you have allowed. Then, in your browser, try accessing http://www.example.com/components/com_foobar/something/test.php (where example.com is the domain name of your site). You should get a 403 Forbidden reply. If you see "You should never see this message" check your settings as it's something that should never happen on a site where .htaccess Maker has run and there was no exception which allows PHP files to run applied in its configuration.