building Qt fails because qmake produces Makefiles with include paths in the wrong order

When qmake produces Makefiles it adds "$(CXXFLAGS) $(INCPATH)" always in that order.
$(INCPATH) contains all the local search paths (e.g. -I../../include/QtCore)
$(CXXFLAGS) can contain search paths produced by the configure checks. In my case when cross compiling thats '-I<SYSROOT>/usr/include'
If <SYSROOT>/usr/include contains a header file with the same name but different content as a header in Qt the one in sysroot is used.
This breaks compiling QtWebKit for me because it uses the wrong pcre.h
Even worse: configure -> compile -> install -> reconfigure with different options -> compile (uses the wrong qconfig.h from <SYSROOT>...

There may be similar problems with the linker search path but I haven't had the time to verify that.