I think I see the confusion here.
Most yards are protected by a signal governing movement into and out of the yard.
They do not necessarily have to be signals on a mast or overhead signal bridge, in fact a lot of yards have dwarf signals, (small single light signals at ground level) which often, but not always display a lunar aspect to allow entrance into the yard.
Lunar signals protect double ended controlled sidings, and most yard throats, although they have fallen from favor lately and are being replaced by the standard 3 light signals.
Lunar aspect indicates proceed at restricted speed, not to exceed timetable yard/track speed.
All a lunar aspect governs is movement past the signal, once past it entering a yard, all switches will likely be hand operated, and where you go is totally up to the yardmaster and the crew.
If, as is often the case, the yard entrance has a single switch that allows movement to two or more lead tracks, so movement must proceed on signal indication past that switch, so your crew, when they pulled out of the one track, entered the circuit governing the signal, which would have made it drop to red for movement entering the yard.
In order to allow the control operator to clear the signal and reline the switch, the crew would have had to pull up to the point the rear car was past not only the signal, but the remainder of the track circuit, to allow the control operator to re-line the switch for the shove movement into the other track.
Most signal systems, when operated in this manner, have a timer circuit designed to allow enough time for a train to clear the next circuit, before they allow the signal to be cleared for a following train, this time out period is normally 10 minutes, once the timer ran it course and unlocked the switch/signal control, the control operator can re-line the switch.
The crew member was riding the rear car to let the engineer know when he had cleared the circuit, and then when the si