Using

• MSVC 2012,
• Jom

MSys2/usr/bin/sh.exe is in the PATH

Configuration

call "%_qt_src_dir%\configure.bat"^
  -opensource^
  -confirm-license^
  -prefix "%_install_dir%"^
  -platform win32-msvc2012^
  -make-tool jom^
  -xplatform android-g++^
  -debug-and-release^
  -no-warnings-are-errors^
  -android-ndk-platform %ANDROID_NDK_PLATFORM%^
  -android-arch %ANDROID_TARGET_ARCH%^
  -android-toolchain-version %ANDROID_NDK_TOOLCHAIN_VERSION%^
  -opengl es2^
  -nomake examples^
  -nomake tests^
  -no-incredibuild-xge

Atfer configure.exe was built and run, the top level Makefile contains

...
MKDIR         = mkdir -p
COPY          = cp -f
..

i.e. it contains commands for UNIX or MSYS shell. The mkdir -p command can not be run in the Cmd shell, because the internal command mkdir has no such option and it has a priority over MSys2/usr/bin/sh.exe.

But if MSys2/usr/bin/sh.exe is removed from the PATH, then the top level Makefile (and others, generated by qmake) has the correct Windows Cmd shell commands.