the 11 foot 8 bridge (which was recently raised to 12ft4in of clearance) was designed to car standard, not to train standard. it was also designed in the 1920s, when the standard for cars was lower. it has nothing to do with the grade trains are on.

I live next to a literal over-under bridge for freight trains where two tracks cross over eachother in order for freight yard operations to not block passenger rail.