Unfortunately at present this is a tricky problem to solve. Ideally we would add a new generator that uses two parallel splines, this is on our to-do list but there are some technical issues that must be ironed out before we can implement it.
In the meantime there are a couple of possible workarounds that may be useful. Firstly, if the geometry allows it, you can telescope the top section of the bridge inside the bottom section. In this example the top section works exactly as described in the bridges tutorial but the RailClone object's z position is moved so that the geometry continues through the ground plane. The pillar base is then added using the same spline but with a surface to position it on the Z Axis. Because this uses the same spline to position both the top and bottom of the pillars, they shouldn't have any problems lining up.
If you cannot intersect the top and bottom of the pillars then the second alternative is to use the technique you suggest.
Using two generators with the RailClone objects Z coordinate between the top and bottom of the bridge you can scale the two halves to meet in the middle. Because of the different spline lengths it will be necessary to position the pillars by adding them to the Corner input instead of Evenly. In this way you can manually add a pillar by creating a vertex of a given type. I would do this for the top spline first to create the correct position and path for the bridge. When this is correct, clone the spline to create the bottom and move the vertices constrained to the Z axis down to the ground plane. Because the vertices line up in the top view, the pillars should align.
I hope this helps to solve your problem, I've attached a simplified demo file to help illustrate. If you have any further questions please let me know.