Simply because it was an issue that I ran into at work. And the reason I focus on arrays is because of the previously mentioned default behaviour of arrays being cloned when passed as an argument for a function. The issue here was someone unexperienced wrote a bunch of code and used only arrays (deep ugly arrays) and it ended up being a huge mess of some references staying the same while others changed. So the only solution was to deep copy at one place. That way later operations on these arrays didn’t affect the original structure. Not pretty but refactoring would have been too much effort.
Sorry for being lazy so no sources for now. But based on my research back then. Using clone (on arrays) is actually slower then json_encode/json_decode.
So there are some cool optimization tricks going on in the background. But that doesn’t make it any more intuitive for me.