Best practices : alpha channel and atlas

I have a 2048 atlas with only RGB info for planks, wall, etc… and some clothes (jacket, pants) with RGBA infos.
I also have an other 2048 atlas with nature stuff (vign, tree, grass, etc…).

I wonder what is the cheaper for rendering for iOS :

-set two atlas entirely RGB or RGBA ?

-mixing RGBA and RGB even if alpha information is a small part of the atlas ?

It would mainly be a texture memory optimization to put the RGB and RGBA textures in seperate smaller atlases.

The shader decides to use or disregard the alpha information on render anyway so there would be no performance hit on the rendering as long as the used shaders are not all alpha blended. But for that, you will create different materials which means no batching.

As long as you don’t have any concerns about the memory usage, I don’t think that it’s worth investing time into. Just go with the way which takes less time and effort.