I attached a small PyQt test case. I found the problem in a C++ app (Gwenview), PyQt is just easier.

I believe the cause is this bit in QXkbCommon::possibleKeys:

// turn off the modifier bits which doesn't participate in shortcuts
Qt::KeyboardModifiers notNeeded = Qt::KeypadModifier | Qt::GroupSwitchModifier;
modifiers &= ~notNeeded;

It looks like this used to work some 10 years ago: https://codereview.qt-project.org/gitweb?p=qt/qtbase.git;a=commit;h=547a1bea492954d828aa0798be93384669812489{{}}

Some digging revealed that MetaModifier was also in notNeeded once upon a time, but that was fixed. Maybe KeypadModifier can also be allowed to participate in shortcuts?