I was able to reproduce this error - I guess its a bug as Qt3D used to build like this. But the Qt folks are probably used to building Qt3D as part of the modular Qt build. My guess is that some part of the qmake step which is meant to set up the header paths is not working on Windows.
I got it to build by copying the headers manually:
# in git bash
mkdir Qt3D
find qt-qt3d/ -name "*.h" -exec cp \{} Qt3D/. \;
mkdir qt-qt3d/include
mv Qt3D qt-qt3d/include/.
Then:
# in VS2012 shell
set PATH=%PATH%;%HOMEPATH%\build\qt5\bin
mkdir qt3d_build
cd qt3d_build
qmake ..\qt-qt3d\qt3d.pro
nmake
Here Qt and qt-qt3d were in the current directory (in qt5 and qt-qt3d respectively) and Qt was built from source already.