It's because humanoid portraits came with their own shipset, and also placed the 'human' portraits in the 'humanoid' portrait category.
Nothing wrong with that on the surface, but I do honestly find it a bit annoying for the CoM, because the more utilitarian ships definitely look better for them IMO. The humanoid ships just look too... Star Treky? I don't know, but I vastly prefer the mammalian shipset for them.
The worst little annoyance is that you can't change it back, or deactivate the humanoid shipset. If you alter the CoM civ and save your changes, it just creates a new custom civ that's identical but uses the mammalian shipset; it doesn't actually change the CoM itself.