That's odd; I never had an issue with my sound in Il-2 when tinkering with the effects
Very strange indeed. To me, chimney and locomotive refers to the smoke used for both. However, it is possible (as you allude to) that they control the effects for more smoke types (for example, if I created a .tga file for the smoke in Il-2, I could change all smoke types to use this file). As .eff files go though, I can't see the benefit of this in game...
Very strange indeed. I wish I could play the game so I could have a look myself! Otherwise, there's not much I can say.