iOS Transparent Texture Question

I’m working on an iOS project and I have a scene that uses one texture as an atlas for lots of objects textures. One of those objects uses transparency.

Is it best to keep it to one texture with a small section which is transparent, or to put the transparent map in a separate texture?

It doesn’t really matter; what actually matters is what shader you’re using in the material. If you only use a transparent shader for the object that needs it, that’s fine. If you’re using a transparent shader for all objects regardless, that’s bad.