I think there is, perhaps, value in a middle ground. You could take the Linux kernel (chosen here for its existing driver support, openness, stable syscall ABI, and presence of virtualization and namespacing features), but throw away basically everything on top of it and build a new "operating environment". Then, over time, you could fork the kernel away, ditching legacy syscalls and features, maybe creating a stable driver ABI finally, etc.
You're missing the point. If the only goal was "functionality," a quick-and-dirty hack on top of existing systems would suffice.
However, the GP wants a system that's reasonably comprehensible all the way down, so he can have some confidence that it's not working against him in some way. The accidental complexity of decades of legacy software works strongly against that.
The Lisp-all-the-way-down part doesn’t seem as useful as it was originally. You could get 80% of the functionality with 10% of the work of a full OS.