A look at molecular assembly
I think molecular assembly will resemble the growth of plants or animal organs. I believe Drexler used the example of a rocket engine in Engines of Creation, a landmark book well worth reading if you are interested in this subject! The engine can’t simply be made from modular reconfigurable microbots and be able to function※. But it is built by such devices. A growth chamber is filled with fluid and swarms of microbots are introduced: they grab on to each other to form a circulatory system and any needed scaffolding. Then raw material is presented in the fluid, and the microbots break up the feedstock to get the individual atoms they need, and start assembling the device. The fluid also bears the fuel and carries away the heat.
So imagine how “bone” is grown. The naturally occurring microbots (called osteoblasts) crawl along a protein matrix and deposit material.
[O]steoblasts produce a calcium and phosphate-based mineral, hydroxyapatite, that is deposited, in a highly regulated manner, into the organic matrix forming a very strong and dense mineralized tissue…
Leaving the circulatory system in place provides for continued self-repair and modification, if provided with power and materials. And the composite structure might be desired for most uses, even with capillaries leaving gaps. After all bone is a very good lightweight material.
But for more solid pieces, the circulatory system can simply be filled in last as part of the retreat of the bots.
※ Having the microbots covered in and contain programmable matter might change this!
About heat
The existence of circulatory fluid bearing raw material and carrying away waste will help matters because it can also carry away the heat.
But what is heat, anyway? It’s random stray motion of atoms. If the atoms and molecules are placed into position very carefully there will be no heat generated! Well, not at the site where it was deposited anyway; it’s a case of Maxwell’s Demon. The circulatory fluid will carry away the extra entropy in some form, to spill heat somewhere else like another vat that needs heating, or a heat sink. (And of course the use of this kind of technology means that energy reclamation systems can spring into existence wherever hot/cold borders exist at the moment.)
So, it’s possible to deposit material rapidly without leaving the workpiece hot. It will be cooled molecule by molecule by damping the excess vibration. Any such assembly needs materials and fuel coming in and waste going out, and excess heat (or entropy) can be among the waste products.
Home environments?
The question specifies “…in home environments”, presuming that home use will be different from business, professional, or industrial use. But the very technology we’re talking about eliminates any such distinction! You won’t have “industrial” installations if the infrastructure is conjured up on demand by microbots. So having, say, a huge vat with pipes and pumps is not something that you won’t have available at home, but will be created on the spot as a kind of temporary scaffolding for the job underway. Any bootstrapping and intermediate steps will simply be taken and not rely on permanent installations of support equipment.
The only real limits will be the logistics of bringing power, feedstock, and microbots to the jobsite. Since the distribution may use the same technology as well, the system will simply add or widen pipes and wires to meet the demand in your location. If you’re conjuring up a house, and need an order of magnitude more supplies than the typical user in that neighborhood, the supplier can enlarge the delivery pipes on the fly because they are made and maintained using the same principles.