That fix means that your apache / php will now check every file across every directory. That'll grind it down a bit more and imagine what will happen on a live server with thousands of visitors..
As for the .html thing, yes there is a reason why we don't recommend it. .html is used for static pages that don't change. .php is used for dynamic pages. If you use .html for dynamic then the webserver has to check every .html page for dynamic content which given enough users and connections will grind it down. Thats why we have the .php extension so that you can choose and switch between resource intensive and non resource intensive.
It's also why it's recommended to use the .htaccess file instead of the main config file for some things because you casn specify different options for different folders. You've just with overkill lol.
If you really want to hide the use of php then just use folder names and index.php file names to mask it. EG:
In each of those folders you have index.php but you never call or link to the php file, just the actual folder. The webserver will serve the index file by default.
My helpful sig has gone because a mod below the administrator gave me an infraction - despite the administrator personally agreeing to it.
If you need any php tips or tricks you can PM me.