Currently, they share the same --target, and we kinda sorta rely on the compiler type. That doesn't allow to build with the MSVC ABI with plain clang (which is theoretically possible), and causes some subtle problems with bindgen. I'm going to address the latter with some short term workaround, and am filing this more long term task to add a comment linking here.
While I'm here, my idea to address this in the long term is to have two distinct target tuples, like the ones rust uses. But a lot of stuff in old-configure currently relies on the "mingw32" part, so even adding support for e.g. "windows-msvc" in the python configure parts currently yields something completely different.