I think the implication is Jack/Vox only took control of the under 25s on Starfleet ships. Bases and the like were not compromised, because they weren't wired into that stupid fleet integration software.
Disagree here. I think the fleet integration software and the transporters were two separate issues. Any under 25s 'in range' of the signal who'd been through one of the transporters would be affected. So there are probably lots of them running around on Earth shooting people.