The current WordPress Coding Standard does not specify which file extensions should be used for PHP files. This proposal establishes that only the .php file extension should be allowed for PHP files. Motivation While web servers like Apache and Nginx can be configured to execute files with various extensions as PHP (e.g., .php3 and .phtml),…

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WordPress proposes standardizing PHP file extensions to only allow .php files in their coding standards. The change addresses portability and security concerns, as different web server configurations (Apache on Debian vs Fedora) handle alternative extensions like .phtml and .php3 inconsistently. Using only .php ensures universal compatibility across server environments and guarantees that code analysis tools like PHPCS will properly check all PHP files.

Coding Standard Proposal: Make it explicit that PHP files must use the .php extension

Or you could just have one index.php as single point of entry… Direct access to other PHP files should be considered as bad practice. The proposal is just a workaround to not address the bad application design of Wordpress.
.php for PHP classes and scripts
.phtml for PHP powered HTML template files