I just noticed this very interesting photo puzzle, and read the posts. Although the thread seems to be 'dead', it seems to be an unfinished topic.
While I am neither a civil engineer nor a local, I suspect the original underpass had a sunken roadway, which from past experience can fill with heavy rains and poor drainage. Perhaps the railroad was impelled to raise the track-bed (as the steel buttresses along the right-of-way suggest.) Then the underpass was back-filled to eliminate the road dip (which would explain the otherwise curious depressions to either side of the road.) As 'Toot' suggests, it would then be logical to put a very heavy load-damping cap on the pilings which support the center span of the bridge. That would minimize the tendency of passing trains to act as pile-drivers, which could result in settling/destruction of the span. It appears the engineers may have calculated this method of support (to reduce the bridge span) to be cheaper than using a much bulkier and longer span, which would have required very robust and expensive bridge abutments, as well as possibly requiring an even higher displacement of the rail bed.
In case anyone has better insight, I would be interested.
Jim W