No. I mean exactly what I posted.
The problem that you display is different, and new compared to an early version of the rivers, as far as I can tell, but maybe I have missed it. Easily done if I didn't try widening the river.
I believe if you compare the river vs rail parameters in the .tra file, something jumps out as noticeable.
Notice that the Alt is used for widening the river while the 4th parameter is not used.
River x,alt,z,?
-82813.976387,102.000000,-11777.063994,00000000
-82813.976387,102.000000,20884.440780,00000000
Rail x,alt,z,?
-87050.418977,0.000000,-11721.271337,00000000
-87050.418977,0.000000,21847.870428,00000000
I've experimented with lowering roads and tracks to -0.5 because I don't like the way they stick up, but it's a lot more work in checking each track.