Last time I checked, software compiled with both Cygwin and MSYS2 internally uses SysV calling convention, only switching to WINAPI when calling, well, Win32 API.

It is more complicated than that. MSYS2 isn't just Cygwin. It has different environments.

MSYS environment is just Cygwin and it uses Itanium IIRC for C and C++ non-Win32 calls since it emulates POSIX. If it links with Windows C runtime they use __cdecl. Win32 API calls always use __stdcall convention / ABI.

However, Mingw environments (Mingw64, UCRT, CLANG etc.) are intended for native Windows development, hence, they use normal MSVC __cdecl ABI for C library calls and internal function calls too. Win32 calls are again __stdcall.

Unlike C, for C++ all MSYS environments use Itanium ABI since they link with GNU libstdc++ or Clang libc++. I think it is possible to use MSVC C++ ABI with Clang but it could be complicated since it requires recompilation of at least libc++.