I don't know the process for certain, but if it's like the Elise and Evora production then all the panels for a car are painted as a set and then fitted to the chassis, rather than building the car and then painting it. So the body-coloured and black parts would be painted separately and then assembled.
The article has confused me, because it talks about the robots being able to open the doors to paint them. This implies painting an already-assembled car but I don't think that's the process.
This is a full panel set for an Evora about to be painted:
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And this picture of a part-built Emira suggests the approach is similar:
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