Unboxed doesn't require multu-unit paint-matching. They could paint the panels and door at the same time and track them afterwards to feed to final assembly so they reunite on the same vehicle. However, that is more of a logistics pain.
Early 2020 Model Y in Pearl White showed signs that Tesla was not tracking simultaneously painted pieces.
Unboxing does require a frame attachment/ bonding system that can be done without damaging already installed paint and accessories.
I think part of the "trick" is not paint-matching parts that don't really need it. So, really only the doors, fenders, hood, trunk lid, and bumpers need paint...and those could be done at the same time and kept together, as you note. But the structural parts of the car that are usually hidden won't need to match in color.
On most cars today, for example, the door frame that is only visible when the doors are open are also paint-matched. Likewise with parts under the hood and inside the trunk. If I remember correctly from the presentation about the Unboxed process, the "normal" way of doing things is basically building the entire car structure with doors attached...painting everything (frame/structure, outer panels, doors, etc.), then taking off the doors (and perhaps trunk lid and hood) to continue with assembly...and then re-attaching the doors at the end. All of the "extra paint" goes away with the unboxed process.
Relatedly, on the Cybertruck, the exterior panels are stainless, and I believe the visible parts of the door frames when the doors are opened are black. Looks perfectly fine visually; it is obvious it's not supposed to match. But it's interesting that the non-visible parts are coated (black, probably for corosion resistance on the structural-steel door frames and pillars), and not matched to the body at all.
If the unboxed process does something similar, with the not-normally-visible parts being left unpainted or just coated some default color for protection, then that's a large piece that doesn't need to be matched back up or tracked with the set. Paint only the visible exterior panels that need paint, batch them for matching and track, and all the stuff that doesn't need to match gets some cheaper/simpler coating and doesn't need to be tracked and matched.
Potentially related side note: I remember there were stories about Tesla having issues painting more and more cars in Fremont because air quality standars limited how much paint could be used. Soon after, every Tesla came with an all-glass roof -- that is a whole bunch of surface area that doesn't need paint anymore. I feel like the limits from the regulation motivated them...and in the end, it's probably a better product with simpler manufacturing. Painting even less of the car in the Unboxed process seems like another leap in that direction.
Or, perhaps the Unboxed process means every car will look like a Harlequin Golf. Every panel a different color, on purpose, so nothing needs to match
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