Great question. It applies to the variant of the spec as it exists today when the license was applied. Currently found at http://facebook.github.io/graphql/draft/
GraphQL's reference implementation (GraphQL.js) intends on not just being a great implementation, but also very closely following the spec, so you're in good shape.
Also, GraphQL.js has had a BSD3+PATENTS license until today, which meant you've always had that patent license. Later today I'll be releasing a version of GraphQL.js that is MIT license instead, understanding that the OWFa1.0 applies to all implementations including the reference implementation.
GraphQL's reference implementation (GraphQL.js) intends on not just being a great implementation, but also very closely following the spec, so you're in good shape.
Also, GraphQL.js has had a BSD3+PATENTS license until today, which meant you've always had that patent license. Later today I'll be releasing a version of GraphQL.js that is MIT license instead, understanding that the OWFa1.0 applies to all implementations including the reference implementation.