Your example is NOT an "interrupt". It is simply an example of "polling". i.e. just going out at some specified time and saying "does this equal that?" Very much different than an interrupt. They could just as easily have said: if digitalRead(5) Then counter1++
In the context of the persons code, it is. "ISD()" is apparently an AVR interrupt command, run on "PCINT2_vect", the Atmega equivalent of pin 5, in the attached libraries.
Your other examples show extentions to the Arduino base functionality. Apparently there are features in the Atmel chip which the Arduino basic language doesn't implement. So they have extentions that you can use to get to those other features. But you must use the special code and syntax. You can't simply use attachInterrupt() as it only supports the pins defined by the definition page.
All of them do. Interrupt pins aren't "hard-wired", like you said, into the Atmega; that's how the Arduino Mega can use the same chip and have more native interrupts. And yes, I understand that I can't use attachInterrupt(), I have to use some variation of ISR(). That's what I'm asking about.