I've been playing around with the categories and currently have this layout. This race doesn't have every type of component, but it has enough to show the principle. I'm not really sure what to do with Command and Control. It seems odd to leave it in its own category, but not sure where to put it. Anyway, I'll take another look in the morning 

I believe this is a very subjective matter, and there will likely never be 100% agreement on how the categories should be defined. That said, I would approach it with a focus on optimizing the structure of the hierarchy. For example, Command, Engineering, and Life Support could be grouped together under a category like "Core Systems" or "Essential Systems", as they are fundamental to the ship’s operation and survival.
Using the same logic, one might argue that Production, Transport, and Logistics could be grouped under "Support Systems" or "Operational Support", since they relate more to resource handling and auxiliary functions.
I’ll leave the final naming to you, as I’m sure there are even better ways to define and label all components.
EDIT: Back to the quote "I believe this is a very subjective matter, and there will likely never be 100% agreement on how the categories should be defined." maybe a toggle group components may help as those who are used to the old ways can keep using their preferred view. Similar to what is currently setup in the colony view tree.