Somewhat less deep than the Alameda corridor floor? Anyway, what does the Alameda Corridor have to do with Amtrak? It is a freight corridor, so this thread should be in the General Rail Discussions forum if anyone else cares enough to respond.
Don't understand the point of the question. The normal overhead clearance requirement is 23 feet above the top of rail. Top of rail to underlying subgrade or bridge deck is normally 24 to 30 inches. I believe the Alameda trench has struts across the top in order to reduce the moment at the base of the retaining walls. How high these are, I do not know. The total desired depth of trench would come from addition of these distances. I seriously doubt it is the same depth throughout anyway.