build: Fixes to restore compatibility with Bazel 9

- Add a missing load of py_binary from rules_python.
- Add missing loads of cc_library from rules_cc in third_party files.
- Inject a missing load of rules_cc in hal_rpi_pico.
- Use .realpath to locate files more consistently with Bazel 9
- Register native_sim as an execution platform for ztests.
- Disable a warning including the C header file
  "zephyr/arch/riscv/csr.h" from C++ code, where a "register" variable
  was used and no longer allowed in C++17 or newer.

Test: presubmit
Bug: 491945168
Change-Id: I4c1bd047c4ec46d1e9e75335eb1785c6f4f73d94
Reviewed-on: https://pigweed-review.googlesource.com/c/zephyr/zephyr-bazel/+/430736