Ah, right after I posted this question a section of the spring data docs caught my eye:
73.5 Configure JPA properties In addition all properties in
spring.jpa.properties.* are passed through as normal JPA properties
(with the prefix stripped) when the local EntityManagerFactory is
created.
So, to answer my own question: prefix the javax.persistence properties with spring.jpa.properties:
spring.jpa.properties.javax.persistence.schema-generation.create-source=metadata
spring.jpa.properties.javax.persistence.schema-generation.scripts.action=create
spring.jpa.properties.javax.persistence.schema-generation.scripts.create-target=create.sql
After doing this, the schema file was generated automatically in the project root.