"Why" and "How come"

One of my friends asked me what is the difference between using “Why” and “How come” and I’m having trouble trying to explain it to her.

Could someone please help me?

How come, when both phrases can be used synonymously in the same structure, is informal; why is neutral register.

How come can be taken as a shortened, fixed form of the archaic ‘how comes it that’, so its integration into a sentence is sightly different than is that of why:

How come you are still sitting here?
Why are you still sitting here?


Thank you very much! This helps a lot!