Issue when initialising

## 🐛 Bug

When I use `indexURL` with the node_modules path for pyodide I get:
```
Error thrown in read:
TypeError [ERR_INVALID_ARG_TYPE]: The "fd" argument must be of type number. Received undefined
```

### Environment

- Pyodide Version: 0.28.0
- Browser version: Node.js
- Any other relevant information:

I'm using it in an AWS Lambda function. The function can also be run locally for debugging.
When running locally, if I don't provide the indeURL path, it tries to load from the wrong folder in my system.
So I point it to the right place (node_modules/pyodide, where the pyodide.js file lives).
It used to work prior to 0.28.0.

### Additional context