Qt for Python (PySide/Shiboken)

Keep in mind flatpak has nothing to do with Qt, neither pyside, so it's completely expected that different tools will have different behavior, and the same way you find problems with one python module, there might be others as well. The same story with others freezing tools, some of them will not work properly. It's a join effort of people filing bug reports in the right place and providing all the details to reproduce and hopefully even a patch to solve the issue.