Take a look in index.php for each application:
/*
* -------------------------------------------------------------------
* CUSTOM CONFIG VALUES
* -------------------------------------------------------------------
*
* The $assign_to_config array below will be passed dynamically to the
* config class when initialized. This allows you to set custom config
* items or override any default config values found in the config.php file.
* This can be handy as it permits you to share one application between
* multiple front controller files, with each file containing different
* config values.
*
* Un-comment the $assign_to_config array below to use this feature
*
*/
// $assign_to_config['name_of_config_item'] = 'value of config item';
I've never personally used this, but it seems to suggest that each separate app can override the settings in config.php using a shared application. So you should be able to do something like this in each individual index file:
$assign_to_config['log_threshold'] = 0;
// OR
$assign_to_config['log_path'] = 'app3/logs/';