That’s quite a lot of mods that I can’t try all. I tried to fix it blindly, so please try the new version 2.0.1 and tell me if it works.
The new version only adjusts the volume of the standard cargo wagon, fluid wagon and artillery wagon, but not modded wagons. If you use other wagons, you can try to enable the option to adjust the sound volume for modded wagons as well. I saw that you have the cargo ships mod installed and cargo ships are like trains, so enabling that option might make ships louder, too.