They were set via the Shopify Admin UI. The values are globally unique and different for each store, so they aren't similar to how the ones in the category tree are exposed. I wasn't able to find any clear approach via API to accomplish the same task...

This may not answer your complete question, but from what I can gather the GraphQL Admin treats "Product Category Metafields" similar to any other product level metafield. In other words, if you request a product's metafields, you will also be able t...