I am going to use texture atlasing for the first time in my games, and at first it seemed like a great idea to split textures into atlases by categorizing them by terrain themes e.g ForestTextures, WinterTextures etc.

But that could cause a problem when for example a flower has to use transparency shader and other models use a diffuse shader. So those cannot be atlased into the same texture. Thus, would atlasing textures into themes as mentioned before and then splitting them by shader like ForestDiffuse and ForestTransparent be good? Or is there a better way to categorize and build them?