Honestly, I should have just made this so I couldn't be misunderstood.
I'm requesting that when you add a new func_model entity, i.e. in BSP or whatever map editor you choose, you can add a key to it along side the keys it currently has. For example, just as you would specify the model key (/models/plants/bigleafx.xxx) you could also specify the skin (/models/plants/y_leaf.tga). But the new key would allow you to select a different skin for the model, i.e. custom textures for plants, different trees using the same meshes, and bright and dark textures for use in different mapping/lighting styles.