You are probably right. All the post-war pictures I have seen show a white command deck; it is likely that the many other illustrations/pictures portraying a brown/dark grey (wooden?) deck are depicting the pre-war version of the liner. The picture below is an example of that:
Note that the two masts have more or less the same shade of gray as the command deck. The same can be seen from the illustrations you have posted below, where the masts are light brown, meaning that they might have been wooden masts. The raking of masts and funnels looks more accentuated then in your model, but this can be just my impression. Also note that the two rearmost couples of vents (near the dummy funnel) are facing the wrong direction in your model.
The following picture dated 12.10.42 shows the ship after her refit as armed merchant cruiser:
Note the absence of the funnel aft, and the replacement of the old masts with two smaller ones, one between the command deck (which, on turn, has a different configuration compared with the pre-war version), and one in place of the dummy funnel. Both funnels and command deck look like painted with medium gray paint (the top half of each funnel being encircled by three darker rings), as opposed to the hull, which apparently sports a lighter shade of gray. Also note the absence of the big vents on the bridge, replaced by a number of bitts and smaller vents, and by the gun platforms. This can be seen better from the model whose picture you had posted a few weeks ago:
Also to be noted the reduction of lifeboats (though from the 1942 picture they are hardly noticeable over the background of the superstructure), replaced by a number of inflatable liferafts on the side of the hull.
Last, two rare pictures of the ship after her late-war reconversion to troop ship (source:
http://furnessbermudaline.com/index_files/Page8257.htm)
Command deck's and bridge configuration don't seem having changed much compared to the AMC version but, as far as I can see from those small pictures, guns and gun platforms have been removed, and the color pattern is more similar to the after-war version (light gray hull, red/black funnels, white superstructure, including the command deck). Also notable the presence of a couple of kingpost cranes forward of the main deck, where the main mast used to be in the pre-war version of the liner.
