The 2000 rpm limit is apparently to do with
'whip' in the crankshaft. The difference in autorotation is that the belts are tense which will probably prevent the whip / lower coupling damage to some extent. If autos below 2000Rpm were not permitted then i doubt the flight manual would mention the risk of throttle chops above a certain DA (i am away at the moment and not near 300 RFM). When the engine rpm is wound down in auto the freewheel unit in the upper pulley allows the rotors to turn, it doesn't slacken the belts and disengage the upper and lower pulley from one another like the clutch would.
I should point out that I am not an engineer so this could be total b****x.
Before rejoining the needles in a C set the rpm somewhere between 2400 and the bottom of the green arc. It'll be much smoother then, although some manual throttle is still required.