I used the "cheese slicer" method for my only major route and initially just eyeballed in contours from a topo map in one window to Trainz in another window, using the Use Elevation tool. Constant referral to an Excel feet/meters worksheet occupying a third window. That resulted in a mapful of ziggurats, or layer cakes, of course. Eventually it occurred to me to use my laptop for the topo map. Better. Smoothing the ziggurats involved using invisible track pinned at the edges of the layers spaced about 25 M apart. Extremely tiresome and it took me from ~Christmas 2009 until 2014 to get enough done I wasn't too embarrassed to upload it.
Since then I've added several baseboards to fill visual gaps, using the ruler grid and invisible track contour lines. Still have to smooth the ziggurats but it's more accurate and goes quicker. An addition can be completed in about a week per board, with scenery etc.
Working in 2009 and 12 the invisible track spline points had to be elevated 0.3 or 0.4 meters to avoid depressing the contours. That doesn't seem to be an issue in T:ANE.
If I ever embark on a real route again I'll get Transdem for sure.
Doing a quickie "test" route that has kind of growed, I've found that the installed displacement maps have too much negative elevation to look real so I create, say, a ridge system with the terrain tools, then copy that as a displacement and reuse it with stretching or compressing the area or altering the proportions. Then the Plateau tool does a nice job of blending the terrain.
:B~)