The Internal GraphQL Server always applies the Schema Configuration defined in its own Settings. This is the case even when executing
GraphQLServer::executePersistedQuery (i.e. if the Persisted Query defines a Schema Configuration, this one is ignored).
The schema configuration for the Internal GraphQL Server is selected in the Settings page, under tab "Server Configuration > Internal GraphQL Server > Schema Configuration":
To make changes, select a new schema configuration, and click on