The FRED 1 and 2 prototypes are not using the 1802 EF and Q flags for tape I/O like most of the CDP1802 machines. Instead dedicated tape HW was build to handle the tape I/O, including logic to start the tape and to detect if the tape is running.
I expect the first FRED 2 prototype included HW to support the 'PM (Pulse Mode) System' as was already introduced for the FRED 1 prototype in February/March 1973. The PM System uses 3.3 KHz tones and identifies '1' or '0' values based on number of cycles (or pulses). A '1' is represented as 5 cycles of the 3.3 KHz tone followed by a 1.2 ms silence and a '0' is represented as 2 pulses.