axa,
The stock manifold is curved to get the carb float bowl level whereas the straight short manifold has the float bowl sitting at too steep an angle. I believe you are going to find the same problem with the direct attachment. Also I checked the interior of the stock manifold and it is pretty smooth. The rubber part of the interior of the manifold is a little rough but not enough to cause a problem IMHO.

Again IMHO the rubber section acts as an isolation zone to reduce vibration and heat to the carb from the engine. Probably a good thing to keep.