The report references two investigations: the FBI's and Special Counsel's. Per the 28 CFR 600.8, Mueller would have authority to investigate the "potentially obstructive" acts committed in connection with Special Counsel's investigation. He would not, however, have prosecutorial authority vis-a-vis obstructive acts committed in connection with the FBI's investigation.
That all being said, Mueller could only prosecute federal crimes - which begs the whole immunity question. But I think it's safe to say that because more of the obstruction was directed towards the FBI's investigation (as I understand, I haven't paid that close attention), Mueller couldn't prosecute.