The point is that the companies decide what production data to deposit on these servers after their legal teams have reviewed FISA requests. According to the tech companies, these requests are individually reviewed and target individuals and are narrow in scope. And they push back when they are broad.
This detail is a major one. This would mean the NSA cannot simply log on to Facebook and query for whatever they want. It means the system is simply a way for companies to comply with FISA requests, something that they were already required to do.
So: even though Twitter doesn't use PRISM, there is really no difference between what the NSA can access on Twitter and what they can access on Facebook. Twitter just complies through some other manner.