The AdditionalConfiguration.php file

Although you can manually edit the typo3conf/LocalConfiguration.php file, it is limited in scope because the file is expected to return a PHP array. Also the file is rewritten every time an option is changed in the Install Tool or some other operation (like changing an extension configuration in the Extension Manager). Thus custom code cannot reside in that file.

Such code should be placed in the typo3conf/AdditionalConfiguration.php file. This file is never touched by TYPO3, so any code will be left alone.

Furthermore this file is loaded after typo3conf/LocalConfiguration.php, which means it represents an opportunity to change global configuration values programmatically if needed.

typo3conf/AdditionalConfiguration.php is a plain PHP file. There are no specific rules about what it may contain. However since the code it contains is included on every request to TYPO3 CMS - whether frontend or backend - you should avoid inserting code which requires heavy duty processing.