WordPress.WP.AlternativeFunctions.file_system_operations error messages cannot be fixed anymore

## Bug Description

`WordPress.WP.AlternativeFunctions.file_system_operations` error messages are overwritten in the ruleset, e.g.

```

File system operations only work on the `/tmp/` and `wp-content/uploads/` directories. To avoid unexpected results, please use helper functions like `get_temp_dir()` or `wp_get_upload_dir()` to get the proper directory path when using functions such as %s(). For more details, please see: https://docs.wpvip.com/technical-references/vip-go-files-system/local-file-operations/

```

However since WPCS 3.0.0 this error can only be fixed by using `WP_Filesystem`. Neither `get_temp_dir()` or `wp_get_upload_dir()` will make the error go away and it's unclear why (unless you debug and find the original error message where it says `WP_Filesystem`)

## Minimal Code Snippet

```php
$f = fopen( get_temp_dir() . '/abc.log' );
```

## Error Code

`WordPress.WP.AlternativeFunctions.file_system_operations_fopen`

## Environment

| Question | Answer
| ------------------------ | -------
| PHP version | 8.3
| VIPCS version | 3.0.0
| WordPressCS version | 3.1.0

## Additional Context (optional)

With `WP_Filesystem`, I think it's unnecessary to overwrite those errors in the first place and these overwrites can all be removed from ruleset.xml

Possibly, errors like `WordPressVIPMinimum.Functions.RestrictedFunctions.file_ops_fputcsv` should be changed to a also only allow `WP_Filesystem` ?

## Tested Against `main` branch?

- [ ] I have verified the issue still exists in the `main` branch of VIPCS.
- [ ] I have verified the issue still exists in the `develop` branch of VIPCS.