When you get down to it, handwavium is the magic that makes the stuff in the setting go. I mean, Element Zero is Handwavium in Fenspace; why not Nanotech? They both fill the same sort of role. They're the magic that lets the high-tech stuff work. I mean, if a two Fen make Healing Potions, does it matter that one's some sort of Handwavium-powered chemical concoction, and one is Handwavium-powered nanobots in a saline solution? If two Fen make General Assemblers, does it matter that one is a 'Waved microwave-turned-Replicator that builds things with teleporters and energy fields, and the other is a 'Waved Washing Machine that contains a swarm of nanobots that build things? Either way, they're both just as magic as the other; they just use different aesthetics to accomplish that magic.
As for needing to assemble things first, well, firstly, that's not technically true; the folks at Grover's Corners 'waved the ground for enhanced solidity just fine before they lifted off. Second, he did use ultrafine graphite particles for a reason. The structures were already there; they just needed to be molded and animated. It'd be like pouring it onto a mass of clay and carbon fibres with a couple googly-eyes stuck on; you'd probably wind up a Carbosilicate Amorph from Schlock Mercenary, and quite possibly the good Sergeant himself.
As for needing to assemble things first, well, firstly, that's not technically true; the folks at Grover's Corners 'waved the ground for enhanced solidity just fine before they lifted off. Second, he did use ultrafine graphite particles for a reason. The structures were already there; they just needed to be molded and animated. It'd be like pouring it onto a mass of clay and carbon fibres with a couple googly-eyes stuck on; you'd probably wind up a Carbosilicate Amorph from Schlock Mercenary, and quite possibly the good Sergeant himself.