While mod support is about a lot more than just changing the models, the point of the question is that we'd need you to give us some way to tell the game to change things. In other words, a way to hook into what models are being used and tell the game engine to use a different one instead. That's completely outside anything to do with Unity.
Generally this means providing some kind of API that would allow us to tell the game engine to change which models/sprites/whatever to load, and add new ones to the game. Ideally there'd be ways to hook our own functions into the games logic and rendering loops so that we can control whatever we've added, or at least into some kind of event system that would let us know when different things happen in the game or when the user does something.
This definitely takes some effort, but has proven to be a huge boost to many games replayability and sales.