In #1497380: Convert shortcut sets to ConfigEntity a new entity type was introduced to represent shortcut sets.
However, the machine name of this entity is 'shortcut'. This is extremely confusing, because throughout the administrative UI a clear distinction is made between shortcut sets (the group of shortcuts) and shortcuts themselves (the individual menu links within the set). I came across this while trying to understand the code, and it took me a while to understand that the code I was reading was actually working with shortcut sets rather than shortcuts themselves.
The entity type should be changed to 'shortcut_set' instead, since that's what it represents.