Walter
You wrote "a special arrangement MAY have been accepted to help helicopters (suitably equipped and with trained crew as was the case in ZD576) in this one awkward turn that would otherwise have complicated a walk-in-the-park/pleasant low level VFR flight on a regularly used leg."
There is nothing awkward about this turn so no special arrangement would be necessary. It is the kind of turn made every day by helicopters (and fixed-wing aircraft) on low-altitude flights. Indeed, this appears to have been a "regularly used leg" (your words) - hardly a likely situation if there was any extra element of risk involved.
Mode 3/A is the standard ATC mode used by all military and civilian transponders. I don't know about the sets fitted to Chinooks, but on some military IFF sets, having the first 2 digits set to 77, irrespective of the settings of the 3rd and 4th digits, identifies to ATC as an emergency squawk. This could have been the intention of one of the crew, indicating that some form of emergency had occurred.
SuperTANS incorporates GPS positioning so why bother with a separate system that, you tell us, gives a range-only readout? Tandemrotor (a Chinook operator) has not heard of the system you describe so it seems unlikely that it's fitted.
THAT TURN
The altimeter is only as accurate as the Regional Pressure Setting (RPS) that is set on its subscale. The RPS is forecast by the National Met Office (nr London) and is notoriously unreliable. This flight was carried out entirely within the Belfast Altimeter Setting Region and the same RPS is used all over it, even though the actual pressure could vary by several millibars within this area - the altimeter is therefore not to be trusted.
The crew had no need to descend over the terrain you have described as they were over the sea at the point at whch the decision was apparently made to turn towards the next turning point. The ground is not featureless - it includes one of the best features available, a coastline. The countdown you have described is not part of Standard Operating Procedures. IF the portable IFF that you have described exists, the fact that it might not be in the position at which you believe it to be is a very good reason not to trust it in the way that you suggest. I believe that your suggestion can therefore be discounted.