Just one more question: Should I rather use qt4 or qt3? Because apparently your script wants to run "qmake", but on Fedora there's only either qmake-qt4 or qmake-qt3!
By the way, the reason why it's always using qatomic_arm.h is an entry in /opt/onyx/arm/include/QtCore/qconfig.h saying:
# define QT_ARCH_ARM
# define QT_ARCH_I386
And this QT_BOOTSTRAPPED is defined nowhere (I made a recursive search through all non-binary files in /opt/onyx/ and in the opensdk-git!). I guess it should be defined anywhere inside of /opt/onyx/arm/mkspecs/, but I can't find, where it would fit logically. Can you maybe do a recursive search through your files, where this QT_BOOTSTRAPPED appears and makes the difference?