I am able to use 4096 textures just fine with mobile devices that support it, like iPad3 & 4. But Unity's packer won't go over 2048, so I am glad you have the option to not use it.
Because it says "if off, use a custom packer" I thought it meant I had to pack them myself using another tool or something. You might want to change the way you are wording that, because I had no idea it just meant to use your packer instead of Unity's. Also, I am surprised you have it set to use Unity's by default when it seems to have multiple issues?