I've stumbled upon a bug reported here:
#6473

If configure my codeception.yml like this

params:
    - .env # load params from .env file
    - env # load params from environment vars

and a value comes both from .env file and ENV variable then the .env value is always used (no matter in which order you load the params).

In the original ticket the issue was fixed in #6477 however only SymfonyDotenv section was changed, could it be that the bug is still in if using PhpDotenv?

Using verions 5.2.2 at the moment:

> php vendor/bin/codecept --version
Codeception 5.2.2