what about vagga
http://vagga.readthedocs.org/
But, since it is still using an OS based package manager (Ubuntu, for example) it doesn't address all of the issues that I outlined. Specifically packages can't be cached across different images by the host. It also isn't obvious which packages are included in which image without cracking the image open.
Thanks for the pointer!
I'm using a common bind mount outside of the container for that now.