Chugman, You are right about a brown color being a much better match than black to go with your carpeting. It is always a challenge figuring out if dust on dark colors or dirt on light colors will be better or worst in any particular environment.
Seeing your photo of the lowered girder bridge area reaffirms my belief that the 20 inch masonite will look better than drapes in that area. Looks like it would be 10 inches of masonite and 10 inches of drapes...which would look strange to me. The transition between that area and the two higher bench work sides could be radiused like your viaduct openings or with a wider leg. I assume the inside curves will follow the cliff / valley terrain to the tracks, roadway, and river below.
Radiusing the inside curves at the control panel area following the curve of the tracks will look great. That one outside curve....well one straight bend in the fascia isn't something terrible especially since it is a 10 inch fascia with drapes below. Plus a building or other item of visual interest on the bench work above the joint will draw the eye away from the joint.
All in all you have this layout very well planned out and it is going to be beautiful.
Paul Goodness