I imagine the production is pretty much centralised in China with everything being dispatched from one location. It makes quality control, set-up and logistics so much easier.
Design and branding again will be handled centrally and fed out to hubs to be localised along with stringent guidelines. The tighter they make it the more they can ensure delivery of a consistent brand.
It will be a monumental effort getting kits made, player images in, proofs back to clubs. If you then threw in custom kits designs the process would be awful and never ending. As it is, once clubs choose their colours they're only agreeing to the right players being used in promotional assets. A studio can then just bash though all the assets and there will be a lot.
At the end of the day Nike needs to make money, people joke about their gear only costing 20p to make but the volume of work to deliver this across the globe for multiple clubs is mind blowing.