Is it possible to have a work around for this new added feature with .56?
The work around would be the bridge / tunnel is now 6x6, with the following coded. A counter is set for each train, when a train enters a bridge / tunnel increase the counter by one. When a train exits a bridge / tunnel decrement that same bridge counter by 1. If the train's counter is greater then 1, then remove then remove the collision mask from the train. if the counter is equal to 0 then return the collision mask back to the train.
Another idea I have seen bantered about on the forums, is the addition of a elevation attribute, i.e. having something above or below ground. That might be another option, by having one of the rails move a train either higher or lower in elevation, and then back to ground level, thereby negating collation where the "z" axis is zero.,
Maybe there are other players / mod developers that have some other ideas to resurrect this mod. Collectively I hope for those that love playing with mods especially this one there can be a way to resurrected Rail Bridges.