One thing is that we are still in the experimental phase of their development. TFP's opinion is that EA means they do their experiments as freely as possible and just make sure that they get a somewhat working version out from time to time for players to inspect.
While they are changing systems around, chances are that many optimizations would be made obsolete by later changes or even counter-productive (as optimizations usually make assumptions about the data that may change later and produce hard to find bugs). Optimization usually is done in the beta or lets call it polishing phase. I would guess they have to really start entering beta in the summer if they want to release 1.0 at the end of the year.
Another thing is that a voxel world put on top of an engine (i.e. Unity) that is optimized for rendering polygons is not optimal. Voxels always have been resource-intensive and were always behind in FPS to conventional rendering engines. While Unity was probably necessary so they don't have to built up everything from ground up, they will have a hard time optimizing anything inside the unity engine. There is a limit to the optimizations they can achieve down there.
My guess is that the amount of voxels that have to be juggled every second is simply bringing the data busses and CPUs on the PCs to their limits. Not much left for all the other necessary tasks like path finding and animation, all of which also need lots of data to be moved.
TFP said they are looking at optimizations but in the development of A17 it seems many of the optimization wins were countered by features that cost cpu and cpu cycles again. Now they might have a hard time finding further worthwile improvements. I'm sure they will be able to still improve the engine in the beta phase but the times where 7D2D would run on a potato are probably over.