[Bug]: __dirname is not hermetic

### What happened?

In some scenarios, the path pointed by `__dirname` is not in runfiles.

### Version

Development (host) and target OS/architectures:

Output of `bazel --version`: 7.1.1

Version of the Aspect rules, or other relevant rules from your
`WORKSPACE` or `MODULE.bazel` file: 1.41.0

Language(s) and/or frameworks involved: js

### How to reproduce

```shell
https://github.com/hunshcn/vitets_alias_broken

bazel run //portal:vite

see output of
```js
console.log(path.resolve('src/'))
console.log(path.resolve(__dirname, 'src/'))
```
```
/execroot/_main/bazel-out/darwin_arm64-fastbuild/bin/portal/vite.sh.runfiles/_main/portal/src
/execroot/_main/bazel-out/darwin_arm64-fastbuild/bin/portal/src
```
This will lead to some strange problems, such as built twice https://github.com/aspect-build/rules_js/issues/1645

Vite is used in this example (because it is found in production). The problem should be reproduced in a smaller way. But because I am not proficient in js, to be honest, I don't even know how cjs/mjs/ts work together directly. I only tried pure cjs without this problem.

### Any other information?

_No response_

Start with the linked vitets_alias_broken reproduction and run `bazel run //portal:vite`. Compare `path.resolve('src/')` with `path.resolve(__dirname, 'src/')` under the reported Bazel 7.1.1 and rules version 1.41.0 setup. Done means the `__dirname`-based path is in runfiles and the duplicate-build behavior no longer occurs.

Written by the indexing model from the issue text.