Now there's some outside-the-box thinking! What I'm imagining though is this simply "mirrors" the problem. Previously it was black or dark colored cars that didn't work. In the proposed scenario it seems it would be white or light colored cars that would be the problem...particularly reflective aluminum finishes like Amtrak cars.
Perhaps the emitter and receiver could separated by an inch or two. It would require modification to the off-the-shelf module...but at least all 'active' components would be on the same side of the track so no wiring across/under the track. By separating the emitter and detector the passing cars would be too close to scatter the reflected light back to the detector.
