Yes, that is unfortunate, and something that we will improve in the future. For now, I really recommend using the metafields endpoint on product_variant to create and update metafields. That way you have more direct control and will get the ids back.
GET /admin/variants/$PRODUCT_VARIANT_ID/metafields.json will give you all metafields on a variant.
POST /admin/variants/$PRODUCT_VARIANT_ID/metafields.json will create a new metafield on a variant
etc.