We're taking it in a fairly different direction from upstream xhyve and bhyve, with the integration with other kits like VPNKit, DataKit (and soon, FSKit). We wanted to be able to diverge the build system in particular, and this makes it difficult to maintain a direct fork.
However, we're committed to upstreaming patches to their relevant projects where relevant, and so the HyperKit Git repository is as close as we can make it. If it diverges a lot in the future with file renames, we'll have to figure out the Git-fu to make cherry-picks easier...