Perhaps the cowling could be retained on the bottom side. It works so well with the shapes it would be a shame to scrap it entirely, but I do agree with the scaling problem. That wouldn't be nearly as serious on the bottom side though, and you did say you wanted to differentiate them. A few greebles (perhaps some antennae and 'sensors', weapons or escape craft tucked into the cowling?) could easily fix the scale problem if it were the less-seen side of the ship where it wouldn't be as immediately apparent.