Build qmake to compile with Windows for Linux

[PhTe]

I have a QT 5.4.1 installation on my Linux System (ARM cpu, qt in folder /media/data/qt5.4.1 ) and i want to write my applications in window.
So i have to configure and build qmake in windows to create matching makefiles for my ARM system.
My folder structure looks like:
C:/Qt/Qt5.4.1/5.4/arm_linux
-- bin Here are the qmake, moc, rcc, and all other exe files (mostly copied from the QT5.4.1 windows version)
-- imports
-- include
-- lib
-- mkspecs
-- phrasebooks
-- plugins
-- qml
-- sysroot The complete sysroot from my target system (qt installed to /media/data/qt5.4.1)
-- translations

I tried
configure -prefix /media/data/qt5.4.1 -debug -device linux-imx6-g++ -platform win32-g++ -device-option CROSS_COMPILE=arm-linux-gnueabihf- -device-option QT_SYSROOT=C:/Qt/Qt5.4.1/5.4/arm_linux/sysroot -opensource -confirm-license -sysroot C:/Qt/Qt5.4.1/5.4/arm_linux/sysroot -o-c++11 -skip webkit -gui -widgets -shared -nomake tests -no-opengl

qmake is compiled, but it searches to moc.exe and all the other binaries in the folder
C:/Qt/Qt5.4.1/5.4/arm_linux/sysroot/media/data/qt5.4.1
not in
C:/Qt/Qt5.4.1/5.4/arm_linux/bin

If i execute configure with -prefix C:/Qt/Qt5.4.1/5.4/arm_linux qmake searches the binaries in
C:/Qt/Qt5.4.1/5.4/arm_linux/sysroot/Qt/Qt5.4.1/5.4/arm_linux/bin

If i execute configure without the -prefix argument qmake searches the binaries in
C:/Qt/Qt5.4.1/5.4/arm_linux/qtbase/bin/qt5.4.1

Which is both useless...

I also tried to create a qt.conf file in C:/Qt/Qt5.4.1/5.4/arm_linux/bin with

[EffectivePaths]
Prefix=..
Binaries=C:/Qt/Qt5.4.1/5.4/arm_linux/bin

But qmake seems to ignores the file. I looked a the persistent values with qmake -query, but they did not changed.

The -set option in qmake can't be used, because i use different QT versions in different folders. As far as i know the persistent values are stored in the windows registry and then they would be used by the qmakes from the other QT versions too which would lead me to wrong pathes there.

So how can i create a qmake which uses the binaries (moc.exe, rcc.exe, ...) from C:/Qt/Qt5.4.1/5.4/arm_linux/bin and all other (includes / libs) from the sysroot folder?