You can either paint a set of panels together off the car and make sure they go onto the same car, or you can run batches of simple colors with low variances between panels and not care which car they go on.

Yeah but handling painted body panels in production is a non trivial effort

They have not yet implemented this process, so it can't be the source of current issues.

You never paint everything at once anyway, so paint matching is a problem always.

You need a highly consistent process either way. Seems to me a smaller paintshop would be easier to quality control. However more parts going individually threw the process also could increase variance.

I would think they care more about saving lots of money then potential paint variance issues. If they happen they will try to fix it otherwise.