-One last thought: Shouldn't the German RR capacity in WitE be cut down in spring 1944, when Wallies started to execute their transportation air bombing plan to prepare second front, and thus decimated roling stock in the Fortress Europa? Is this build in WitE?
I wanted to actually look into this part of your post in a little more depth. I got hold of a used copy of a book entitled: "The Collapse of the German War Economy, 1944-45" by A.C. Mierzejewski. The book focuses upon the Allied Strategic Bombing campaign on the German Transportation System and the resultant effects on the German Wartime economy. And yes I would agree that the game engine neglects this outside stimuli and its potential impact upon in-game Axis rail capacity. However, it's probably debatable as to when such effects should begin to manifest themselves in-game as well as how much turn by turn degradation in rail capacity should be occuring as a result of "off-map" stimuli.
Treading down this pathway would -- IMHO -- require that a similar assessment be made on Soviet in-game rail capacity and various stimuli affecting it. Moreover there are numerous unmolded aspects of the Soviet transportation system that should – realistically – be affecting turn-to-turn Soviet rail capacity.
Given how extremely crucial railroads and rail transportation were to both the Soviets and Axis I'd argue that in terms of simulation modeling, rail capacity should be treated with a similar level of complexity (or greater level of complexity) as Truck transportation within WiTE. Moreover, there could be a pool for locomotives and rolling stock (the rail capacity value) that is subject to break-downs and destruction just like supply trucks. In addition, drawing upon rail capacity to move factories or troops means fewer locomotives and associated rolling stock being available to move supplies to font line units, or to move coal, or iron ore to steel manufacturing facilities, or to move oil or fuel, etc etc. Ying and Yang. You can’t move 70,000 troops by rail along with all their equipment and supplies without there being a trickle-down effect upon every other aspect of a both everyday logistics flow and the wartime economy as a whole (maybe instead of trickle-down effect, I should say a landslide effect).
Well WitE rail pool, I think, does simulate rolling stock. What it does not do is taking into account rail line capacity, like numbers of tracks. But this would be very complicated to simulate, because you'd have to assign capacity per RR hex.
As for non-military and non-factory-evac rolling stock use, I just don't know if & how this is modelled. Probably not at all.
But at least one thing about RR system IMO could be reconsidered, that is the time it takes to build solid, drift ice proofed RR bridges over major rivers. One week is not enough. Consequence would be that major offensives would fade out more quickly - for both sides due to supply issues.