So if you are making any kind of reusable design, you cannot annotate your classes with @Bean anymore. Instead you will make an @Configuration (like spring boot auto configuration) that by discretion may pull in some more general (not @Configuration annotated) reusable configuration. Since some classes will be considered implementation details, you won't want to expose those into the dependency injection container of spring (since that is equivalent to making them public, people will inject them and depend on them!). So instead you will only create them inside your own @Configuration and pass them directly when generating an @Bean from a method.
Congratulations, your @Configuration is manual dependency injection. That is easy enough. Why did we need inversion of control over the dependency injection in the first place? It isn't immediately obvious to new engineers what aspect of the @Autowired is dependency injection and which aspect is inversion of control. Many of us don't see much of a benefit to the inversion of control if you are taking care of your application's hygiene in the first place.