3 Rail Fan, unfortunatley this is nothing new and Lionel has done this a good many times in the past, so I wouldn't hold it against them.And not only have truss bridges and tunnel portals been a problem, but so hasn't the clearnace height of the elevated trestle sets... some cars will not clear these.
Adding to the problems, is the new trend towards scale sized cars. I'm sure some of the companies like Atlas 0, make their accessories like these, more full scale to accomodate their larger cars. Remember, most older postwar/MPC Lionel cars are undersized in precise scale height and width.
From personal experience, I found a similar case with the Lionel Flat Car with Derrick Crane. I was remaking one into a Conrail MOW car with other added features and details. Before I starter the process, I found the derrick crane, when the support part was left fully engaged in an upright position, would not clear my Lionel snap-together truss bridge. So I cut the molded simulated wheel part off the top of the derrick support, chopped some length off the support and then glued on the very top simulated wheel part that I had cut off. Then I repainted the whole thing. It clears everything on my layout just fine now.
The other possibility (and an advantage of the snap-together truss bridge) is to make a new base for it out of basswood, with raised sides to heighten the clearance of the whole bridge.