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.