Building with clang doesn't work when Qt headers are in a system header location

app-id: org.pyside.Test
runtime: org.kde.Platform
runtime-version: '5.11'
sdk: org.kde.Sdk
modules:
  - name: pyside2
    buildsystem: simple
    build-commands:
      - python3 setup.py install --prefix=/app
    sources:
      - type: archive
        url: http://download.qt.io/official_releases/QtForPython/pyside2/PySide2-5.11.1-src/pyside-setup-everywhere-src-5.11.1.tar.xz
        sha256: 9cbc3cbb03c6c1ddba8de7a651c84b269f87ebd4a0991a1f9acc8b2d0ccdfb83

$ flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
$ flatpak install flathub org.kde.Sdk//5.11
$ flatpak-builder --install build_dir org.pyside.Test.yaml

[...]
qt.shiboken: (core) enum 'QMetaMethod::MethodType' is specified in typesystem, but not declared
qt.shiboken: (core) type 'QItemSelection' is specified in typesystem, but not defined. This could potentially lead to compilation errors.
qt.shiboken: (core) enum 'Qt::CursorShape' is specified in typesystem, but not declared
qt.shiboken: (core) type 'QEventLoop' is specified in typesystem, but not defined. This could potentially lead to compilation errors.
qt.shiboken: (core) type 'QVariantAnimation' is specified in typesystem, but not defined. This could potentially lead to compilation errors.
qt.shiboken: (core) type 'QTemporaryFile' is specified in typesystem, but not defined. This could potentially lead to compilation errors.

qt.shiboken: (core) No C++ classes found!
qt.shiboken: (core) writeMinimalConstructorExpression: Could not find a minimal constructor for type 'QByteArray'. This will result in a compilation error.
qt.shiboken: (core) writeMinimalConstructorExpression: Could not find a minimal constructor for type 'QModelIndex'. This will result in a compilation error.
Done, 712ms, 362 warnings (3 known issues)
[  2%] Building CXX object PySide2/QtCore/CMakeFiles/QtCore.dir/PySide2/QtCore/qabstractanimation_wrapper.cpp.o
c++: error: /run/build/pyside2/pyside3_build/py3.5-qt5.11.1-64bit-release/pyside2/PySide2/QtCore/PySide2/QtCore/qabstractanimation_wrapper.cpp: No such file or directory
c++: fatal error: no input files
compilation terminated.
make[2]: *** [PySide2/QtCore/CMakeFiles/QtCore.dir/build.make:527: PySide2/QtCore/CMakeFiles/QtCore.dir/PySide2/QtCore/qabstractanimation_wrapper.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:354: PySide2/QtCore/CMakeFiles/QtCore.dir/all] Error 2
make: *** [Makefile:128: all] Error 2
error: Error compiling pyside2
Error: module pyside2: Child process exited with code 1