If the iOS application has already paired with a BLE peripheral that has gone out of advertising mode, can it connect using only the device-specific UUID, retrievePeripherals, and connectPeripheral?
If not, is there only one mode that the peripheral can advertise in, or are there varying levels of privacy/identification that can be set when advertising?
No, it cannot. To create a connection to any peripheral device, that device would have to advertise using connectable advertising. The device that wants to connect, will then have to reply to one of the advertisements with a connection request.