To summarize that paper:
The only time flex came close to galv steel was fully extended and there was considerable loses when at 94% efficiency, which is extremely rare (i've never seen it) in the field.
Expect to see flex duct losses approaching 50% compared to galv metal; in addition, expect to see losses using ductboard with liners more than 33% compared to metal(ASHRAE design manual).
From a techs point of view, my experience shows that ductboard & flex systems lower seer ratings 2 to 3 points with all the deteriorating effect that low-airflow systems give(too numerous to mention here).