Olin,
That bridge footing was for a later highway crossing and is not C&L related. I too thought this was the case for many years. Recently I was able to photograph the original survey map of the line at the Californai State Archives and found The railroad crossed nearly in the same location as the modern highway. The "grade" that runs parallel to the highway is one of the old roads.
The Meriam Library at Chico State has a photo showing this arrangement:
The house seen on the hill was the home of the Colusa Sandstone company superintendent.