They can represent anything you like, you can have a variable y if you want.
If you are referring to the system of coordinates that command like getpos and setpos use ... they come in the form [x,z,y] where x is north-south and z is east-west. Or the other way around, I can never remember. y is up-down, or height.
This is a Cartesian coordinate system. The origin is at the SW corner of the map. Your post refers to a polar coordinate system, which of course you can use (Sui made a post on how to convert from one to the other only today) but it is not really built into the game.
Nobody knows why BIS decided to describe it as x,z,y instead of x,y,z. Or if they do they aren't telling. Well, ok, its just me that doesn't know. ;D
If you look under common array formats in the official command ref - its a special topic - you will find out more.