Environment variables are generally fine for secrets. Environment files are problematic. Modern systems that inject secrets into the environment launch the program itself.
I'm not sure I get the difference - the issue I would have thought was having the system code have access to the secrets themselves? Env file vs env vars injected at runtime seems the same there - either can be exfiltrated. The difference would be having it injected when used.
Is the problem with files about what happens outside that, being committed, etc?
The headline here is that there's no reason to believe "environment variables" were the reason this data was breached; presumably, the database those variables came from was what actually got hit.
These problems were all solved a long time ago.
We have a couple of VMs that are not mission critical, and they don't hold sensitive data. We just inject the secrets into the runtime. Access to those machines is restricted to a single IP, there's not much more protection in front of them.
A meaningful attack on one of those machines would require a LOT of effort, and almost nothing in return. Some systems don't NEED to have government level security, as a developer it's my job to provide the best solution for each scenario.
(IE, I wouldn't put 12 security cameras and an armed guard around a fruit stand, but I might around a jewelry store)