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What is the filesystem engine? Is it just something fancy on top of NFS, or something completely new?

It's something new.

Is it related to the work started by Brad Fitzpatrick a few months ago with the goal of implementing client-server gateway between the host and the guest filesystem using FUSE?

The new daemon (dubbed osxfs) is FUSE-based at the moment, but also provides a semantic translation layer between OSX filesystem calls and Linux kernel events. The FUSE layer can be removed in the future in favour of a direct kernel module with this architecture, if it ends up being a bottleneck (its fine right now though)

Do you use a custom protocol between the daemon running in OSX and the one running in the container?

Is there some kind of caching? If yes, what is the impact on tools like make when checking atime or mtime? If no, is there a perceptible impact on latency, for example when compiling a large project in the container?

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