But there's a difference between confusion that arises because something is complex or inconsistent and confusion that arises because people have the wrong mental model.
"I assume that SQL tables are basically just fancy CSV files. Therefore strong invariants are obviously confusing."
If most serious users have the wrong mental model about something, then either there's a serious documentation/training failure, or the correct model is non-obvious and counterintuitive (or both). Blaming the users for their ignorance is not productive in either case.
But if the file you are removing is the only reference (i.e. hard link) to that inode, you're not just modifying the directory's contents; you're also removing data from the filesystem as a whole.
That comment comes across as very arrogant. Of course if you're familiar enough with the system then you'll have no need to read this, and you can go off and seek gratification installing Gentoo and telling everyone about it.
But some people don't know, and benefit from learning it. So chill.
My mental model is that a directory is just a special file that links to other files.
Adding or deleting a file to a directory is just a case of writing to the "special file" to add or remove links to other files.