Answering my own question. This is not an issue with spring boot, but with the bean dsl syntax.
It must be beans { }. Not beans = { }
Removing the equals sign loads the configuration fine. I was using the Grails way of resources.groovy, where the syntax is beans = {}
Also, in order to inject the Config.groovy, I had to use
new ConfigSlurper().parse(Config) instead of new ConfigSlurper().parse("Config.groovy")
where Config.groovy is a file in the same directory as bb.groovy.
(Ref: http://docs.spring.io/spring-boot/docs/current/reference/htmlsingle/#cli-groovy-beans-dsl)