Specifically, the way a mental model of a hierarchy is broken by mounting a higher-order ressource (UEFI variables) as a subordinate of a file system that is itself a subordinate of the OS.
UEFI vars are just hardware resources. Mapping them as a file system object is just unnatural and, yes, stupid.
Trying to use a permission model ("only root can do it") overlooks the real problem: The user do not expect higher order objects to be mapped as subordinates of the file system.
When you delete from the file system, you expect objects to be deleted from the disk - not UEFI variables to be altered or deleted! And because the user does not expect such behavior, there's a good chance she/he will override warnings and go ahead with the operation expecting only file system objects to be affected.
This is "everything is a file" taken a bridge too far.