Mods overriding other mods is a fact of mod life. Load order determines which wins out. (See: Skyrim/Fallout)
This is largely a byproduct of database design. If the game used a relational database and the tables were designed accordingly, we could do things like change only the MinLevel of an item without overriding all properties of that item. Similarly, we could insert only a subtable without overriding an entire treasuretable.