 Interestingly, for me it seems the Super key is named "Super_L" and most importantly can be used as a single key. The keybinding Primary+Super_L actually works on its own. Once I would add a third key to the comvination, the Super key will get a modifier but on the combination of two modifiers, it is a single key.
So, on my system, the current behaviour seems correct to me. It just raises the question why is this behaviour different and what components have any impact on it?