There already are some files in the various included packages with the .inc.php extension.
We use WinMerge to compare changes between versions and allow for integration of our specific modifications. Making bulk extension changes would make the upgrading process much more time consuming. If such a change is being made a new major version number needs to be established.
The change can't be done merely by overlaying the current version since such would leave behind the .inc files and no security hole has been closed.
Web server security needs to be properly set if the pages are being served on the internet.