Is the on-orbit assembly of the transfer “stack” assumed to be performed robotically? If not, does the human assembly crew have to live in the torpor-optimized habitat during assembly operations?

Yes, the baseline architecture calls for robotic, on-orbit assembly. Note though either way, between the crew transfer vehicle (e.g. Orion), the habitat, the pressurized docking node, and the Earth Return Vehicle (ERV), there is still a lot of habitable volume available.