Flatpak SDK: gtksourceview-3.0 doesn't build (due to g-ir-scanner)

Hello! First of I hope this is the right place to ask.

I am trying to build a flatpak app with org.gnome.Sdk//42 and gtksourceview-3.24. The app itself is running via Python and powered by PyGObject.
However it seems that something with gobjectintrospection doesn’t quite work with that version:

At the end of the build for gtksourceview:

  GISCAN   GtkSource-3.0.gir
Traceback (most recent call last):
  File "/usr/bin/g-ir-scanner", line 98, in <module>
    from giscanner.scannermain import scanner_main
  File "/usr/lib/x86_64-linux-gnu/gobject-introspection/giscanner/scannermain.py", line 35, in <module>
    from giscanner.ast import Include, Namespace
  File "/usr/lib/x86_64-linux-gnu/gobject-introspection/giscanner/ast.py", line 29, in <module>
    from .sourcescanner import CTYPE_TYPEDEF, CSYMBOL_TYPE_TYPEDEF
  File "/usr/lib/x86_64-linux-gnu/gobject-introspection/giscanner/sourcescanner.py", line 34, in <module>
    from giscanner._giscanner import SourceScanner as CSourceScanner
ModuleNotFoundError: No module named 'giscanner._giscanner'

Relevant module from the flatpak XML:

  - name: gtksourceview3
    config-opts: ["--enable-gtk-doc=no"]
    sources:
      - type: archive
        url: https://download.gnome.org/sources/gtksourceview/3.24/gtksourceview-3.24.11.tar.xz
        sha256: 691b074a37b2a307f7f48edc5b8c7afa7301709be56378ccf9cc9735909077fd

Gobjectintrospection is the one provided in the SDK. I was successful in getting everything to build with an older version as a sub-module (1.63), however that breaks PyGObject, so downgrading it doesn’t seem to be an option. Is there any workaround or configuration flag I am missing?