Ok, short example. Both the axis medium model and the sniper wear a field cap. Now what I want to do is lets say built a medium model that wears an officers cap but keep the sniper with the field cap.
Now what I want to know is if the "look" of the classes is hardcoded or if there's a way to determine which submodel group are used for each body part.

I don't think you're able to change what submodels a model uses. Because my experiences say it's hard coded.

But here's what you can do. Delete the field cap model(But make sure you save it some place). Then on the axis medium body submodel, or legs, or whatever it uses, merge the officer cap on that. Then on the sniper body submodel and yadda yadda, merge the field cap on that. Assign verts and compile.

Edit:

Make sure that the submodels you pick are exclusive to that class and not other classes. I don't know if there is such an option. Cause that would suck. But you'll have to check anyway.