You're supposed to add B3D Model objects for different model files. That's how it's designed to work.
If you were trying to do something like a model viewer or level editor (did you mean that by "customize the level"?) this would indeed become a problem. Something like the "Override" action of the box behavior could remedy this.
Again though for a regular game it's not necessary. I'll see about bringing "Override" to other behaviors/plugins.