Hand assembled, all the way.
The are varying degrees of what needs to be built in order to assembly a prototype vehicle, depending on the degree of change from existing models. For example, a new vehicle may use an already existing engine, or a modifed version thereof. Therefore an engine (or other already-good-enough subassembly) can be ordered directly from the plant that makes it, making many parts really quite cost-effective to procure.
In other cases, mass-produced parts that are “close to” the part the engineering team really wants are bought off the line and modified so that they work.
Additionally there are a large number of job/fabrication shops (some belonging to the manufacture, many outside the company) that do small batch runs. Say you need a few deck lids – company will design some dies, some sheet metal will be stamped, and you have some very expensive doors, deck lids, fuels tanks, whatever. Eventually these dies or others will end up in a “real” stamping plant for mass production.
Even cars touted as “as all new” typically are evolutionary rather than revolutionary, so a lot of the super-expensive, high-precision stuff doesn’t have to necessarily go through the same, small job shop runs.
Sometimes plants are all new. Sometimes plants are retooled, which means add kits to what’s already there, or rip out everything and start from scratch. Starting from scratch takes longer, and you lose the ability to build what you’re already building. Kitting can often be done on an off shift, or during a scheduled plant shutdown in a lot quicker time. So the first true production vehicles can roll off the line with very little loss. These pilot vehicles typically will not be sold to the public but use for all kinds of internal purposes.
The increasing use of flexible automation will soon make it possible to do much of the model change changes in software. Dump the new program into the PLC and robot, put the parts on the line, and (theoretically) start building the new model right away.
Oh, FWIW: low production vehicles are sometimes hand assembled. The EV1 was completely hand assembled in the Craft Shop in Lansing, MI.