I really think that this is the case. Splitting the data would involve considerably less people in the know than asking for cooperation. Also, only the telecoms were granted immunity. The NSLs really appear to be solely for metadata, and maybe the uniformed response to this program by the 9 companies listed is a diversion from the NSLs, and they have not given "direct access".
It makes even more sense when you consider the name of the program "prism" is an object that's capable of splitting light into it's colorful components, i.e. decoding the data streams into visible readable more colorful data streams. Each company is a color exposed by prism.