You dont need to worry about application instances and isolation because application will be created [each time](https://github.com/yiisoft/yii2/blob/master/extensions/codeception/TestCase.php#L31) before test.
You also can mock application in some other custom way, for this purposes you have method [`mockApplication`](https://github.com/yiisoft/yii2/blob/master/extensions/codeception/TestCase.php#L55) available in your test case,
this method will create new application instance and replace old one. Use this method when you need to create application with config that is not suitable for all other test methods in current tests case, for example: