py_zipapp duplicates shared libraries

# 🐞 bug report

### Affected Rule

The issue is caused by the rule: `py_zipapp_binary`

With the following settings

```
common --@rules_python//python/config_settings:bootstrap_impl=script
common --@rules_python//python/config_settings:venvs_site_packages=yes
common --@rules_python//python/config_settings:venvs_use_declare_symlink=yes
```

### Is this a regression?

No

### Description

Shared libraries that shipped in pip packages are duplicated in the zipapp, once in the venv path and once in the wheel run files path. For native heavy packages, such as torch, this can significantly increase the size of the resulting zip file.

This is related to the closed #3439, but there the issue was packaging the run files using third-party rules.

The run file layout has both paths as symlinks pointing to the real file, but when building the zip file one is created as a `symlink` and the other as a `root_symlink`. These are added separately into the zip manifest and don't get deduped `tools/private/zipapp/zipper.py` and instead get byte-copied into the zip file.

I would expect these to be deduped, so that only one copied into the zip file and the other becomes a symlink to that.

## 🔬 Minimal Reproduction

```python
# BUILD.bazel
load("@rules_python//python:py_binary.bzl", "py_binary")
load("@rules_python//python:py_zipapp_binary.bzl", "py_zipapp_binary")

py_binary(
name = "demo",
srcs = ["demo.py"],
deps = ["@pypi//grpcio"],
)

py_zipapp_binary(name = "demo_zip", binary = ":demo")
```

```bash
$ bazel build //:demo_zip
$ unzip -l bazel-bin/demo_zip.pyz | grep cygrpc
2419632 1980-01-01 00:00 runfiles/rules_python++pip+pypi_311_grpcio_.../site-packages/grpc/_cython/cygrpc.cpython-311-x86_64-linux-gnu.so
2419632 1980-01-01 00:00 runfiles/_main//_demo.venv/lib/python3.11/site-packages/grpc/_cython/cygrpc.cpython-311-x86_64-linux-gnu.so
```

## 🔥 Exception or Error

No exceptions or errors

从 tools/private/zipapp/zipper.py 和 issue 中的 py_zipapp_binary reproduction 开始。运行 bazel build //:demo_zip，使用 unzip -l 检查生成的归档，并比较两个 cygrpc 路径。当 shared library 只复制一次，另一个路径表示为 symlink 时，即视为完成。

由索引模型根据 Issue 内容生成。