Respect `include-system-site-packages` in layered environments (#11873)
## Summary
We use a similar strategy to the ephemeral overlay: set
`include-system-site-packages` in the `pyvenv.cfg`, and clear it
whenever we access a new environment.
Closes https://github.com/astral-sh/uv/issues/11829.
## Test Plan
Difficult to test because we don't really have support for system
packages in our test infrastructure. But...
```
> uv venv --system-site-packages
> ['', '/Users/crmarsh/.local/share/uv/python/cpython-3.13.0-macos-aarch64-none/lib/python313.zip', '/Users/crmarsh/.local/share/uv/python/cpython-3.13.0-macos-aarch64-none/lib/python3.13', '/Users/crmarsh/.local/share/uv/python/cpython-3.13.0-macos-aarch64-none/lib/python3.13/lib-dynload', '/Users/crmarsh/.cache/uv/archive-v0/AhKcORkaCdbBl31VweRtG/lib/python3.13/site-packages', '/Users/crmarsh/workspace/uv/foo/.venv/lib/python3.13/site-packages', '/Users/crmarsh/.local/share/uv/python/cpython-3.13.0-macos-aarch64-none/lib/python3.13/site-packages']
```
```
> uv venv
> ['', '/Users/crmarsh/.local/share/uv/python/cpython-3.13.0-macos-aarch64-none/lib/python313.zip', '/Users/crmarsh/.local/share/uv/python/cpython-3.13.0-macos-aarch64-none/lib/python3.13', '/Users/crmarsh/.local/share/uv/python/cpython-3.13.0-macos-aarch64-none/lib/python3.13/lib-dynload', '/Users/crmarsh/.cache/uv/archive-v0/AhKcORkaCdbBl31VweRtG/lib/python3.13/site-packages', '/Users/crmarsh/workspace/uv/foo/.venv/lib/python3.13/site-packages']
```