Apparently, importing ~/.config/kglobalshortcutsrc is enough for the shortcut to show up in the System Settings, but not enough to load the shortcut. Disabling, applying and re-enabling and applying again also doesn’t help, and neither does re-assigning to the same shortcut, which resulted in this lovely error dialog.
This 15 year old post on AskUbuntu explains the differences between those keys, and their historical background: https://askubuntu.com/questions/19558/what-are-the-meta-super-and-hyper-keys
Gotta love those legacy paradigms. Thanks for the link!