You can always use closures (anonymous functions) to get any kind of params you want to any place you desire.
See here: Multi Tenant Multiple Database Setup
What I would do is to use a caching server like memcached, make sure you cache the values after you read them from the DB, you really do not want the same queries to be run over and over again. Afterwards use a closure to merge the data that you have read and cached from the DB to any default values you have while still using the same config files.
If you really want to speed things along in your index.php file, when reading the config you can create your own config array any way you desire (I would still use memcached) and start the application with that config. The config files are basically just arrays that are used when starting the application.
1 thing, you probably cannot use any yii specific functions in either place because the Yii application will be available until after you start it (with a config I mean) so you might have to create the functions in PHP directly.