Short Stack, Invisible/Vanishing Paint
"Invisible Paint" in alpha -
Assuming this is like some of Ben's other steamers, you'll find it's set up so you can customize the tender and cab side lettering using alpha masking, that is, there's an "alpha" layer in the TGA files provided for those areas so you can substitute your own road name and number.
The trick (which I learned figuring out how n8phu modified one of my creations to substitute better couplers) is to make an alpha mask/layer for the main texture map, too. This would be (IMHO) a three-step process: first find the smokestack's source area on the main texture map TGA and eliminate the top of it by masking it (everything else remains unmasked). This is like using invisible paint.
Next, create the lip at the top with a bright line at the very top of the unmasked part and a dark shadow somewhat below it, and save your modified texture map with alpha layer using your paint program.
Finally, you need to add a line in the main texture map's texture text file in the asset file. The added line will indicate that the alpha layer is in the same TGA file as the main texture, but without it the alpha layer will be ignored. (I'm not at my hobby machine right now so can't give the exact wording - look at the texture text file for the changeable road name on this or another loco.) Commit the loco with the changes, and you should have a short stack with a satisfactory-looking lip at the top.
The one problem you may have is that ths smoke source attachment points will be higher than optimum because they're placed for the higher stack. This is OK, really, because there are a lot of variables to real-world smoke and it sometimes doesn't appear instantly at the top of the stack anyway. It's also possible that there's a separate area which is being used to color the *inside* of the stack, which you'd have to find and also mask. The symptom of this would be a black "ghost" tube visible only from the inside.
Have fun!