Take a look at System/Boot...line 144
(new DotEnv($paths->appDirectory . '../'))->load();
This is not working, just tried a fresh download of 4.6.1. I suggest the code is updated to read from the Paths.php file as well.
in the Config/Paths.php
public string $env_directory = __DIR__ . '/../../';
Then in System/Boot.php
(new DotEnv($paths->env_directory))->load();
This simple update would fix them problem and allow the framework to be used in creative ways. The env file used to be loaded from the index.php file, if it's put in the Paths, just like all the others, it will be helpful.
Thanks