When you allow direct access to a .php file you are only letting the file run i.e. not get blocked by the front-end or back-end protection. The other options of the .htaccess Maker still apply to this file.
For what is worth,
SIMPLE options like myOption=myValue are NOT blocked. However, if you would try something which is a file path it would be blocked by "Protect against common file injection attacks". If you use a complex hash which is similar to
PHP's easter eggs then the "Disable PHP Easter Eggs" feature would prevent it from running. Likewise, if you have enabled "Block access from specific user agents" and you're using one of the user agents listed in "User agents to block, one per line" in whatever tries to access that PHP script then you will also get blocked.
Try disabling some of these options to see what is actually blocking you and then think why the user agent string of the client trying to access the file and/or the parameters you are sending in GET or POST are triggering one of the protections you have enabled in .htaccess Maker.
Nicholas K. Dionysopoulos
Lead Developer and Director
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