Why does an Arduino MEGA 2560 have different PORTS
Thats because Arduino has configured the Mega to do so. In microcontrollers you need to select what use will each pin have based on the availability. To make user interface easy arduino has done this based on what is commonly used by everyone. Even then some functions are still not disabled. 

For example 50,51,52,53 are SPI pins on mega which use Pin change interrupt for working. Thus it not necessary we use them for SPI we can also use them for Pin change interrupt. 

Similar is the case for pins 10,11,12,13. These PWM pins can also be used for Pin change interrupt but other PWM pins cannot.