I think if you look at the finished model in the context of a C2 freighter and think "the deckhouse is too tall for a C2", you won't like it. On the other hand, I look at it as a "360' long ship that could be", much like Howard Lloyd's model pictured here which also has a deckhouse the height of which has about the same relationship to the length of the ship that my model will. For my purposes with the HO trains, I'm going for the impression of a cargo ship that "could be", not an exact scale rendering of any particular ship in the same way that Lloyd seems to have done.
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Lloyd started out with a Dean's Marine "Melanie 2" kit in 1:96 scale, but if you look at the photos it appears that he may have made the deckhouse taller because the HO scale people on the upper part of the deckhouse don't seem out of scale.