Update run-qmake template to run Orbit configure.py first, followed by mkspec export. This should allow hb SYSTEMINCLUDEs for subsequently processed .pro files.
<?xml version="1.0"?>
<project name="SF-PACKAGE-REFS">
<path id="sf.spec.system.definition.files">
<fileset dir="${sf.spec.job.drive}/" casesensitive="false">
<include name="${sf.spec.systemdefinition.location}"/>
</fileset>
</path>
</project>