> That only works when all your systems run the same kernel, on the same architecture, using intercompatible versions of system libraries
If dotfiles aren't compatible across OS kernels, you're doing something wrong. I keep scripts in ~/bin under VC, but with anything that needs to be compiled I just track the source and build with make (or emacs, etc.). You don't need to put everything in ~/bin in the repository!
From the summary, I don't really see how the system would work transparently across OS X, Linux, and BSD. It looks like it expects git + Ruby + OS X, and I don't use the latter two. (I prefer Lua and OpenBSD, respectively, but that's me.) Also, I work with i386, amd64, and occasionally sparc, and the platform thing isn't an issue since I'm not syncing binaries.