Craig, I think you have half a valid point. Why not recycle your waste, if it can be done well? However, it seems more likely in the NASA program that premade protein powder would be one of the fundamentals of the printing palette. I would guess 75% of their objective in this design is to streamline and compact the onsite food storage and production stream.
That protein could certainly come indirectly from waste, via such routes as canister farming of legumes, etc. But that is something best left for an area where water and operating room is not at a premium, such as a base on the Moon.
That's pure speculation at this point, although I'm sure a moonbase will feature gardens and farms.
3d printing is well-proven, and what interests me are the possibilities of foodCAD....