The ;label breakers' requirement, I think, is a good example to illustrate where good design differs from poor. and how poor design cannot be 'fixed' by the rule book.
Let's face it ... by the time you're labeling the breakers, the damage has already been done.
The first nightmare is commonly found in residential construction, where the same circuit is used to power both sides of a wall. In practice, this has often meant that the common wall between the living room and the dining room was on one circuit, while the common wall between that same living room and a bedroom were on another. Try describing that clearly in the panel directory!
Another example is the lighting; while often on separate circuits, the circuit hops all over the place - again, often resulting in a difficult situation to describe.
The second nightmare comes up in 'tenant improvement' work, where commercial suites are divided, combined, walls are added and removed, receptacles are added and removed, over time. I had one place where, when I killed a circuit to tie in a new receptacle, a receptionist three offices (and two panels) down the hall lost her computer!
The only real way to keep this from happening is to ... stop taking the easy way out. Yesterday, I had a mini-mart ask me to quote adding some sign receptacles over the front windows. Sure, I could just tie into any convenient circuit - how much power do beer signs use, anyway? - but that just might setting the stage for a real problem later. If nothing else, it would complicate the ID at the panel. The only way to 'do it right' - and clean up some prior messes, address some other issues, as well - is to redo a few other circuits at the same time, all the way back to the panel.
Naturally, this in turn means doing the work while the business is closed - or at least, not very busy. Say, 3-10AM Sunday. I can hardly wait