CMake and setup.py are not synced since nanobind transition

Since moving to nanobind from pybind11, the newest CMake options are not synchronized with setup.py. 

For example, `py_limited_api` is set separately in both [CMakeLists](https://github.com/onnx/onnx/blob/main/CMakeLists.txt#L474-L477) and [setup.py](https://github.com/onnx/onnx/blob/main/setup.py#L321-L343), so if I want to disable abi3, I need to patch in both setup and CMake.


