What about the lowering of COG? I assume it was less but was it still attempted (by landing on bended knee)?
I haven't read the study, but what you're saying here is slightly wrong. Lowering of the COM does NOT occur because of landing on a bent leg. It happens after contact, during stance. Landing on a bent leg would seem to have the same effect as contacting on the ball of the foot. It allows for too much amortization of the leg during the penultimate step, thus decreasing velocity and not allowing the jumper to "get out" of the step into their take off.
COM lowering happens during stance, not at or before contact.
To second what mike said, I also teach the flat-flat. I find that, while it does tend to decrease velocity a little more, it helps to transfer the speed of the approach into the take off of the jump. contacting a penultimate on the ball of the foot seems to me like it would also be a little too risky injury wise. Trying to lower the COM on a foot that is still up on the ball seems like it would be too unstable and risk the athlete getting hurt.