TYPO3 Core

I do not think, the method is supposed to be called like that. The function signature and the doc block (https://github.com/TYPO3/typo3/blob/v11.5.27/typo3/sysext/core/Classes/Configuration/ExtensionConfiguration.php#L127) suggest it should be called like this:

$extensionConfiguration->set('myext', ['myvar' => 'myvalue']);

...
'EXTENSIONS' => [
        'myext' => [
                'myvar' => 'myvalue'
        ],
],
...

$extensionConfiguration->set(
    'myext', 
    array_merge(
        $extensionConfiguration->get('myext'),
        ['myvar' => 'myvalue']
    )
);

...
'EXTENSIONS' => [
        'myext' => [
                // ... whatever was set here before
                'myvar' => 'myvalue'
        ],
],
...

Please note that `set` is explicitly marked as internal and should not be called in an extension.
If you want to provide extension configuration, you should usually use https://docs.typo3.org/m/typo3/reference-coreapi/11.5/en-us/ExtensionArchitecture/FileStructure/ExtConfTemplate.html

The Core PHP Code ExtensionConfiguration.php also says:

"This API is however OK to be called from extension manager hooks."

The ext_conf_template.txt was insufficient in this case. The customer needed a solution to set configuration variables from within the extension via a simple form (without access to the entire Typo3 System as an editor-user). Therefore $extensionConfiguration->setAll was choosen.

For example updating an E-Mail address for cronjobs.

But I think this issue can be closed because I used the wrong signature of the set method.