Some combinations of modifier keys can't be assigned via the UI keyboard shortcut editor:

e.g.:

Ctrl+Option+Shift+Cmd+[A-Z]
Ctrl+Option+Cmd+[A-Z]
Option+Shift+[A-Z]
Option+Cmd+[A-Z]
Option+Shift+Cmd+[A-Z]
Ctrl+Option+[A-Z]

You can use them in the json file, but not via the UI.