In the config.ini.php, it is not possible to set a configuration settings in a config file without setting the whole category in this config file.
We should have some sort of merging that would make possible to set only a sub configuration variable from the global.ini.php into the config.ini.php. This way, during an upgrade, we could keep only the config/config.ini.php and overwrite the other config files with the updated piwik version and we would keep the user changes.
Example
In global.ini.php
[Test]
value1=test1
value2=test2
In config.ini.php it is NOT YET possible to change only value1 doing something like
[Test]
value1=test1edited
Currently the user has to paste the whole category to change only this variable
[Test]
value1=test1edited
value2=test2
