Many aftermarket turbochargers and superchargers are designed to work on your stock engine internals. However, swapping out pistons, valvetrain, etc. allows for more boost which means way more power for you! One of the most crutial aspects of forced induction is unimpeded airflow... the more restrictive your airflow, the less power. So, cat-backs make much more difference on a FI engine rather than a NA. Same with air filters. Where as you'd get like 2hp from a nice filter with an NA engine, you'd get 10 with a FI.
In a nutshell, it's way easier to make power when your working with forced induction. Cost efficiency goes through the roof... the hard part is saving the money for the turbo/sc.