A couple thoughts:
First: Thread does have a device layer, and it's ZigBee's. I think only the device descriptors themselves are borrowed, the goal being to not only give Thread a proven device layer, but also to make it easy to port devices from ZigBee to Thread. I know this has been approved, but I'm not sure if it has made it into the current Thread specification (which I haven't seen).
Second: You want a "reference" stack all the way down to the hardware? That's not a "Reference Implementation" in any sense I'm familiar with. That's just an "implementation". "Reference" = "Proven Correct"
The best reference implementation is hardware-independent, and is actually a simulator. The goals are to have the reference implementation be highly instrumented, so that problems with either the protocol or the reference implementation itself can be easily identified and debugged, and also be highly portable.
When I've had to make a true Reference Implementation I almost always use a scripting language, in part to improve productivity by keeping all the code very high-level, but also to make it perfectly clear that this is NOT something to ship in a product!
It is then trivially easy to have the simulator run on a workstation, with input and output redirected to raw sockets, that is then connected to a candidate low-level microcontroller with it's own protocol implementation. We expect the microcontroller implementation to have problems, but those problems become shallow (easy to solve) when the simulator is available. I, for one, intensely dislike debugging protocols on microcontrollers that can't support real-time debugging, which is the case for most microcontrollers.
Finally, a true "Reference Implementation" is an essential tool for exploring changes or additions to the protocol, making it easy to try things out without having to run any compilers or flash any microcontrollers.
So, where is the real "Reference Implementation" for Thread? That's what I'd like to see shared with the community. With a common reference, good targeted implementations will pop up like popcorn,