If your bonding rate is 100 nanometers per minute, and layering in 2d, a 1 cm thickness is going to take 100,000 minutes. That's 69.44 days. And assuming you can have a tip head that operates on every single possible atomic space at once. That's even not realistic - it would be more like 1000 times slower (190 years) than that (to make room for a 33x33 atom tip) if the layer is not uniform (if the layer is uniform - say 1 layer of cobalt - you can go faster).
So basically 2d layered 3d "Atomically Precise Nanomanufacturing" using an inkjet like technology would only be "fast" for very thin uniform things that could easily be assembled into larger/thicker things by chopping them up and stitching/gluing/bonding them together.
Admittedly filling a void with a liquid and letting all the individual molecules bond to each other is a different animal (and can happen concurrently) but if you need the item to be precisely laid (with a lot of variation) out down to the atom it's still going to be incredibly slow/expensive to produce.
P.S. This is a continuation of what I'll call my "singularity delayed due to faulty back of the envelope calculations" series some previous stuff at http://eclipsephase.com/fast-moving-nanites-are-not-hard-sci-fi http://eclipsephase.com/anti-nanite-weapon-flamethrower
"I fear all we have done is to awaken a sleeping giant and fill him with a terrible resolve."- Isoroku Yamamoto