doc: note --env-file is not applied to --run

Environment variables loaded with `--env-file` are not applied to the
command executed by `--run`. Document this limitation under `--run`.

Fixes: #62988
Signed-off-by: Paul Bouchon <mail@bitpshr.net>
PR-URL: #64442
Reviewed-By: James M Snell <jasnell@gmail.com>
Reviewed-By: Luigi Pinca <luigipinca@gmail.com>

Author: bitpshr

doc/api/cli.md

@@ -2688,6 +2688,9 @@ The following environment variables are set when running a script with `--run`:
 * `NODE_RUN_PACKAGE_JSON_PATH`: The path to the `package.json` that is being
   processed.
 
+Environment variables loaded from a file with [`--env-file`][] are not applied
+to the command executed by `--run`.
+
 ### `--secure-heap-min=n`
 
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