It is a good decision. Fact of the matter is when designing airplanes they are usually designed as simplistic as possible and not to take into consider every what if scenario.
I know the big jets don't really ever in formation very often (although I have seen a few cool pics from South African
) but when flying in formation only the lead would have their transponder on.
In the event of an engine failure we turn the TA/RA mode to just TA so you still produce mode C just won't have an RA. It's probably simpler to design a transponder that is fully controlled by us rather than hooking it into other systems (like AS or WOW switches etc..)
Perhaps when the results of this mystery is known insurance companies may want a GPS tracking option on all airplanes? Hard to say.. Transponders only work if they are close enough to a secondary radar facility.