I am wondering what the best place would be for a Spring Boot app to register additional beans. I have a Main class that is annotated with @SpringBootApplication
Yes, including your beans inside the @Configuration class is usually the preferred way for Spring.
This is also one of the ways Spring recommends injecting inter-dependencies between beans is shown in the following sample copied from the Spring's reference guide here:
Additionally, the default scope of @Beans is SINGLETON, if you specify a different scope such as PROTOTYPE the call will be passed to the original method. Have a look at this section in the Spring Reference Guide