I just stumbled upon changes made in #16416.
Since the Flex command is neither deprecated nor replaced by the core one, I find the description confusing (the core command is not part of Flex).
Also the "new" way requires more boilerplate and is not optimal, to run the command the dotenv files needs parsing, whereas when using composer it can be done before running any console commands.
I suggest to document both ways, explaining why the old one is optimal, and why the new one can be necessary.

I you agree, I would be happy to take care of it.