ATX specifies where the [CPU] is on the mother board, the size of the [PSU], the position of the screw holes in the motherboard, the power connectors, where the holes on the back of the case should be, where the connectors on the front of the motherboard (for the front lights and buttons) should be etc. 

  

 While it was an excellent standard when conceived, it has aged. [ATX] was designed with the excellent idea of modular components, incl each being responsible for its own cooling. Unfortunately, modern computers tend to have much more demanding cooling needs than once upon a time, and cooling components individually is a recipe for noisy systems. An integrating approach to cooling that addresses the needs of multiple components, f.ex using a HeatPipe, drastically reduces both the flexibility of the design on the one hand as well the noise on the other hand.