There is a philosophy that long forcing cones work best with long chokes - see the new SL2 and the monsters supplied with it. The contrary might be true . . .
I recall Muller also suggesting that 3 & 1/2 inches was an ideal length so their chokes were extended to allow for that length overall; their standard invector ones stuck out 2 inches as a result which might account for what you have seen.
Look at Blaser, Krieghoff and Perazzi and their chokes are shorter and I have no doubt will ideally match the barrels they produce.
In most cases it is marketing hype and you are better off sticking with the factory supplied chokes or those made by a recognised name - I have found no difference between the Brileys (as supplied) & Teagues in my Blaser F3 and I'm using Teagues given I will avoid the USA as much as possible going forward.