TYPO3 Core

I can confirm with 10.4.14. But in my case the value is just written in case the key does not exist in LocalConfiguration.php. If it exists, but value is different, nothing happens. Maybe that helps to find the cause.

Unable to reproduce with core v10 and master (instance without many fancy extensions).
This is probably not the SilentConfigurationUpgradeService: Operations in there avoid AdditionalConfiguration, but it still would be interesting on what actually causes this.

As side note: Using AdditionalConfiguration has no great core support and is risky for the install tool in general since install tool by definition can't handle arbitrary code people hack into this file. Considering the fact this is early bootstrap, it's an additional risk for system stability, especially when upgrading.
I remember a strong warning about this file but can't find it anymore ... the docs should be adapted accordingly.
Also see my comment on https://forge.typo3.org/issues/93818#note-1 on how this could be improved so this file could be dropped in most if not all cases.