Well, this isn't anything I have any real authority on, but could it be that the plates have changed since then? There are now high-cube containers, which may be taller overall than equipment in the recent past. Also, longer (53') containers, which may mean a little more corner overhang. I don't know what the AAR plate standard for doublestack equipment was 15 years ago, or its relevance to the Donner route. It may now require a larger overall plate, necessitating tunnel modifications or the exclusion of equipment on some routes.

Also, as an aside, car kind M3F (think Automax) is limited to 13 MPH in Tunnel 3 on the Stockton Sub, but not tunnels 1 or 2 and no tunnel restrictions for those cars over the Techachapi grade. Those car designs are about 9 or 10 years 'new' to the industry.