ModuleNotFoundError raised using flask run command but not in vscode debug

Question

I have a flask app, the structure tree is like:

./backend
│   .ENV
│   Config.py
│   run.py
│
├───app
│   ├───Main
│   │      routes.py
│   │      __init__.py
│   ├───Models
│   │      db.py
│   │
│   ├───ToConGenerate
│   │      routes.py
│   │      utils.py
│   │      __init__.py

I have Flask initialized in Main/__init.py file and run.py file is the entry point of the app.

#run.py

from app.Main import app

if __name__ == "__main__":
    app.run(host='0.0.0.0', port=4200, threaded=True, debug=True)

In the Main/__init.py file I import database instance using from app.Models.db import db. The blueprint definition is in the ToConGenerate/__init__.py.

Now if I debug in vscode, everything is fine. But when I use the command flask run in virtual environment, I get error ModuleNotFoundError: No module named 'app' in the Main/__init__.py file. I know there must be something run with the launch.json file but I cannot figure it out.

The virtual env is handled by miniforge3.

The launch.json is like

{
    // Use IntelliSense to learn about possible attributes.
    // Hover to view descriptions of existing attributes.
    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
    "version": "0.2.0",
    "configurations": [
        {
            "name": "Python: Flask",
            "type": "debugpy",
            "request": "launch",
            "module": "flask",
            "python":"C:\\Users\\zz\\AppData\\Local\\miniforge3\\envs\\ZZ39\\python.exe",
            "env": {
                "FLASK_ENV":"development",
                "FLASK_APP":"${workspaceRoot}/backend/run.py",
                "FLASK_DEBUG": "1"
            },
            "args": [
                "run",
                "--no-debugger",
                "--no-reload"
            ],
            "jinja": true,
            "autoStartBrowser": false
        }
    ]
}

In the .ENV file I set

FLASK_ENV=development
FLASK_APP=run.py

Can someone help and tell me where I am incorrect?