I'm also having issues with transparency in atlas creation. The resulting image is a 24-bit PNG instead of a 32-bit one, so the alpha is completely discarded. Furthermore, the "Alpha Is Transparency" toggle gets unchecked on all the textures that are added to an atlas, which disables their transparency. This means if they're used elsewhere in the project, they lose their transparency and this also breaks Unity's preview of some textures - for instance completely white icons, where only alpha channel varies become completely white and it's impossible to visually tell them apart.
Using Unity 2017.3.0f3 + NGUI 3.11.4. Attaching the actual output and the source images I arranged in what would be a desired result (checkerboard added for emphasis).