Not being willing to spend the time required for a detailed analysis, my rough take is as follows. (You need to follow the link in the OP.)
Molecules approaching from the left will, for certain angles, be more likely to be guided throught the holes. However, the steeper the wall angles, the less likely it will be for molecules approaching at an angle off the perpendicular to reach the hole. They will rattle around in the well and then bounce out. For molecules approaching from the right, there is no enhancement for some angles, but also no shielding for others. I suspect that the two just happen to cancel out.
Also note that there is at least one case where the funnels do absolutely no good: perpendicular approach and 45 degree walls. Any molecule which bounces off a wall will do so at a 90 degree angle, then bounce a second time at 90 degrees and exit the funnel right back the way they came.