As I understood it, from Mark Read's letter to the FIA, they believe it will take more distance to decelerate the car than it will to accelerate to maximum speed. A symmetric track, e.g., one with the traps in the middle, would have to be excessively long. Using two traps allows each to be positioned closer to the start, allowing for a shorter track.
The rule allowance for parallel tracks would take care of the per-run course damage, as you point out.
Tim