My personal preference is to have my lanyard above the block sling and my climbing line below. I usually use an srt system for my climbing line, so if it does get pinched by the sling, I can still decend. Also, I make sure my climbing line is snugged up under the sling so it cannot come in contact with the block or the moving rigging line. As stated in Marks article, the block coming down under load can sever, or at least damage, a climbing line and a moving rigging line can burn the climbing rope. I like lanyard above because I fell it gives me a more comfortable position, and if the block sling slides down on the lanyard, there is the potential for me to be stuck. Since my climbing line is below the block sling, it can't be bounced over the top. If my lanyard is bounced over the top, my climing line will hold me.
One other thing I would like to add. I run my lanyard on the lower d's of my tree motion. Not everyone likes that, for me its more comfortable and I have better ability to move my waist and thus my whole upper body. An added bonus of that setup is that in the event of a trunk splitting or a big peal down, my lanyard and bridge make a closed loop that I am not contained within. Hopefully everyone reading this has heard the term "circle of death" referring to the harness and lanyard to hip d's where you could be crushed inside of durring a trunk split or peal down. With the lanyard to the lower d's on a rope bridge saddle, no circle of death. A potential downside is that if the rope bridge is broken by the split or peal, the climbing line is no longer attached to the climber. I think it is unlikely to happen, but it is a potential. A solution is to make sure the lanyard is less strong than the bridge. I think the stock treemo bridge is stronger than most lanyards, but I am now going to look in to that. Also as I write this, it occurs to me that it is also unlikely to be an issue if there is a block properly tied to the tree as the sling would take the brunt of the split or peal, depending too on the way you attach your block.