Graham:
While I appreciate your enthusiastic tinfoil-hattery as an amusing diversion, I really must take issue with your chain of reasoning and conclusions.
My understanding is that this device is to the current wafer process what waterjet CNC systems and 3D printers have been to physical manufacturing. It makes small-batch runs affordable. This would be an incredible boon to small manufacturers and hobbyists, as it would enable them to do things on silicon on a smaller scale than is currently possible, which means more designs and experiments will be made and tested.
It has nothing to do with "slipstreaming" malicious changes into a normal production run. For one thing, normal production runs will almost certainly continue to use the current wafer process, as the economy of scale catches up quickly there once the masks are made. For another thing, making any changes to the layout of an ASIC requires at the very least that the entire chip be re-floorplanned, timing checked, etc., which is neither trivial nor guaranteed to actually work. It's actually much easier for entities to get your malicious routines inserted in the current model, by working together with the proprietary mega-chip designers behind the scenes in the first place.
Besides, if this device fufills it's promise, I'd look forward to a growing community of open-source ASIC plans that you could have chipped out by the reputable company of your choice, after you review them for malicious government transistors. And, when it's discovered that Motorola backdoored your cellphone for the government for you, it's at least possible that a company or group could get together and spin out a compatible yet safe version of the chip in question (something that the high costs of masks prohibits currently).