Nitro build does not add native externals that are required.

### Environment

Node v24 and Nitro v3.0.1-alpha.2

### Reproduction

Reproduction in test of linked PR.: https://github.com/dake3601/nitro-cjs-trace-repro

### Describe the bug

Importing cjs package that requires a native external will not be in the bundled output.

### Additional context

See #4094 for more info.

### Logs

```sh

```