Project contains three textures that are in same sprite pack and in different asset bundle variants. However sprite packing still happens.
Its not fully a bug more like a feature request. There was some debates in slack #devs-2D char, so they decided it to put as "3 - Workaround is possible".

Project Steps:

1. Open the project
2. Select Window | Sprite Packer
3. In the Sprite Packet window, click 'Pack'
4. You should see this: http://gyazo.com/a4c33e8400b0d2a3798d5b2db817d3dd - i.e. all of the sprite variants end up in the same atlas

Workaround:

- Just don't pack sprites if they will end up in different asset bundles.