Most of what goes on on most bases is as unsecret as it gets. The rooms where sensitive things happen have security measures in place and they keep you from bringing your phone in there. Usually a little locker is provided where you store your phone while you are inside the protected area. In some very sensitive places there may be additional active and passive measures but usually people with access to those areas police themselves.
Like a lot of data collection, the meta data gets you pretty far. The who's and where's can be hoovered up with tracking data buys and essentially get you a nice list of who has access to certain areas, which can be used for targeting individuals.
