The basic idea is still valid. You might just have to use a more appropriate mechanism when using containers. For example, the explanation of the Config factor explains that a config file can also be used.
I guess you avoid the risk of accidentally logging secrets with other env variables but otherwise it seems to be just as secure/insecure.
It's a pretty fine distinction and I don't know how many people actually bother doing SELinux etc. in practice, but theoretically it's marginally better.
Bonus: you can watch the file for changes. Which means your app can pick up rotated secrets without a process restart, whereas if you inject secrets via the environment they're fixed for process lifetime.