What are you trying to save here? Disk space? VRAM?
If you cared about VRAM usage, you don't have much choice but to use PVRTC / DXT textures. In my experience DXT isn't generally as horrible as PVRTC, but still very noticable.
On the other hand if you weren't too bothered about VRAM usage, but cared more about disk space, there is one more fairly viable option - keep the atlas images as PNGs. I had a user contribution for this, but not had the chance to integrate completely + test all possibilities. This will trade of some additional main memory & load speed, for a massively reduced disk footprint.
Vote for it on the trello if you'd like it implemented sooner
https://trello.com/b/UfqlXqXy/2d-toolkit-roadmapThis isn't a complete solution to solve everything though - ultimately, you're making some pretty serious trade-offs, main memory + load speed. It would be much better if Unity compressed assets as it does in the webplayer or at least had the option to do so... Try building your project for webplayer and see how small it is.