sip seems to include it own copies of qt's qmake(.conf) bits, but they seem
generic wrong in some places.  

Wouldn't it make sense to use qt's known-good versions?  If so, include
something like this snippet in sip's specfile (before actually building it, of
course):

unset QTDIR || : ; source /etc/profile.d/qt.sh
for target in default linux-g++ linux-g++-32 linux-g++-64 ; do
test -f $QTDIR/mkspecs/$target/qmake.conf -a -f specs/$target && \
 ln -sf $QTDIR/mkspecs/$target/qmake.conf       specs/$target
done