Texture Atlas Duplicating Because Of Material Differences?

I employed the use of texture atlas in my game and gave myself a pat on the back for optimizing my game and following best practices...

But then I read something somewhere about how I was actually duplicating my textures in GPU memory because of the wide range of materials and shaders I was using. My texture atlas contains a wide collection of sprite images, particle images, mesh texture images, decals, GUI images, etc.

And because some materials I use have transparency, others have color tints, etc... that I was not really leveraging the one texture atlas but was, in fact, causing a huge texture memory waste because the same texture atlas was actually loaded multiple times?

Can someone set me straight?

Developing for iOS with Unity5.

Thanks, Manny