It is pronounced the same way. But the meaning is different:

“Pourquoi” is more about the cause and “pour quoi” the purpose.

“Pour quoi faire” can also be formulated “pour faire quoi”. Which helps making the nuance more obvious if relevant.

They are homonyms but the meanings are different: “pourquoi” means “why” and “pour quoi” means “what for“. But they are effectively pronounced exactly the same way.

“Tu es venu pourquoi faire” n’a aucun sens en français; à partir du moment où on est convaincu de cela il n’y a plus à se poser de question sur des différences de sens.