Yes, I sometimes do this myself to create a simpler boundary. You can set the Opacity to a lower value and the boundary will still be calculated.
What do you see if you set DebugMode on the PhysicsController? Does the boundary look correct?
Another possibility is that you are seeing tunneling. This is an issue in Farseer 2.x and should be fixed by Farseer 3.x (if you search for tunneling on the farseer forums you will see what I mean, objects can pass through each other if they are moving too
fast or you do not have a small enough TimeStep)