Failing to run compiled Python extension

Also “MSYS Makefiles” strikes me as odd (you can’t (reliably) invoke other Cygwin forks from Git Bash directly). You probably want “MinGW makefiles”.
And the fact that you override parts of the toolchain – whether it works or not, it’s clearly an unsupported setup.

FWIW, there’s now official guidance on how to invoke commands in MSYS and MinGW environment. I don’t know if CMake makes that unnecesary by setting up the correct environment for you or not.